Electron Coupling Calculation with CDFT and CDFT-CI approach

Hi everyone, I calculated the electronic coupling for the same donor–acceptor system using standalone CDFT/direct coupling and CDFT-CI, but the resulting coupling values differ significantly. In both calculations, the Becke charge and spin populations satisfy the intended constraints. When I compared the Hamiltonian matrices, the main differences appeared in the diagonal terms, Hii​ and Hff​. In the Q-Chem manual example for CDFT/direct coupling, the first two jobs generate the two constrained diabatic states, while the third job evaluates the coupling using the HF method. My concern is that, although the diabatic energies are obtained at the DFT level in the first two jobs matched what I got from CDFTCI, the HF calculation in the third job seems to produce different Hamiltonian elements. Could someone clarify the methodological difference between standalone CDFT/direct coupling and CDFT-CI? I am sharing input files for both the approaches.
CDFT:

$molecule
-1 2
   C       2.68641000    -0.43326000    -3.93764000
   C       3.38058000     0.91782000    -4.20888000
   C       3.88034000     1.57322000    -2.90874000
   C       2.72404000     1.74215000    -1.90951000
   C       2.02042000     0.41030000    -1.64388000
   C       1.52629000    -0.23478000    -2.94239000
   H       3.42781000    -1.08212000    -3.43973000
   H       2.67521000     1.59934000    -4.70460000
   H       4.22598000     0.77975000    -4.89228000
   H       4.60695000     0.88516000    -2.45426000
   H       2.00089000     2.46157000    -2.31674000
   H       3.10554000     2.16857000    -0.97495000
   H       1.18068000     0.56197000    -0.95716000
   H       2.71878000    -0.27357000    -1.14247000
   H       1.04697000    -1.19576000    -2.72540000
   H       0.75978000     0.41525000    -3.38853000
   C       2.25567000    -1.10964000    -5.22643000
   C       2.84670000    -2.29619000    -5.68842000
   C       2.50041000    -2.90277000    -6.88317000
   C       1.49838000    -2.35947000    -7.75749000
   C       0.89327000    -1.15153000    -7.26645000
   C       1.26325000    -0.57238000    -6.06821000
   C       1.14280000    -2.96018000    -9.00827000
   C       1.75445000    -4.17331000    -9.49510000
   C       1.41855000    -4.73603000   -10.70929000
   C       0.44908000    -4.16064000   -11.55417000
   C      -0.17225000    -2.97871000   -11.10424000
   C       0.14944000    -2.40119000    -9.89321000
   H       3.62104000    -2.75294000    -5.07277000
   H       3.02019000    -3.81591000    -7.15817000
   H       0.11586000    -0.66244000    -7.84643000
   H       0.77260000     0.34635000    -5.75248000
   H       2.51075000    -4.67285000    -8.89666000
   H       1.92245000    -5.65094000   -11.01885000
   H       0.19003000    -4.60890000   -12.50805000
   H      -0.92947000    -2.50081000   -11.72468000
   H      -0.37179000    -1.49141000    -9.60928000
   C       3.96112000     3.93809000    -3.78835000
   C       4.59658000     2.88220000    -3.17431000
   C       5.95256000     3.04289000    -2.78334000
   C       6.62711000     4.21570000    -3.00699000
   C       5.98553000     5.31114000    -3.64104000
   C       4.62669000     5.16572000    -4.03783000
   C       3.97688000     6.25790000    -4.67557000
   C       4.64518000     7.43306000    -4.90580000
   C       5.99812000     7.57698000    -4.50946000
   C       6.65142000     6.54104000    -3.89232000
   H       2.92236000     3.84608000    -4.09783000
   H       6.45850000     2.21250000    -2.29785000
   H       7.66500000     4.31989000    -2.70211000
   H       2.93941000     6.14358000    -4.97804000
   H       4.14020000     8.26083000    -5.39386000
   H       6.51489000     8.51308000    -4.69656000
   H       7.68927000     6.64618000    -3.58755000
$end


$rem
   METHOD = wB97M-V
   BASIS = 6-311+G**
   GUI = 2
   SCF_MAX_CYCLES = 800
   CDFT = true
   CDFT_PRINT = TRUE
   CDFT_BECKE_POP = TRUE
   CDFT_THRESH = 8
   BECKE_SHIFT = UNSHIFTED
   THRESH = 14
   S2THRESH = 14
   SAVE_SUBSYSTEM = 10
   POINT_GROUP_SYMMETRY = False
   SOLVENT_METHOD = PCM
   MEM_TOTAL = 248000
   MEM_STATIC = 4000
$end

$cdft
 1.0
 1.0  17 37
 1.0
 1.0  17 37  s
$end

$pcm
   THEORY                CPCM
   heavypoints           590
   method                swig
   radii                 bondi
   solver                inversion
$end

$solvent
   DIELECTRIC  7.5
   OPTICALDIELECTRIC  1.97
$end

@@@

$molecule
 read
$end

$rem
   METHOD = wB97M-V
   BASIS = 6-311+G**
   GUI = 2
   CDFT = true
   CDFT_PRINT = TRUE
   CDFT_BECKE_POP = TRUE
   CDFT_THRESH = 8
   BECKE_SHIFT = UNSHIFTED
   THRESH = 14
   S2THRESH = 14
   SAVE_SUBSYSTEM = 20
   POINT_GROUP_SYMMETRY = False
   SOLVENT_METHOD = PCM
   MEM_TOTAL = 248000
   MEM_STATIC = 4000
$end

$cdft
 1.0
 1.0  38 54
 1.0
 1.0  38 54  s
$end

$pcm
   THEORY                CPCM
   heavypoints           590
   method                swig
   radii                 bondi
   solver                inversion
$end

$solvent
   DIELECTRIC  7.5
   OPTICALDIELECTRIC  1.97
$end

@@@

$molecule
 read
$end

$rem
   METHOD = HF
   BASIS = 6-311+G**
   POINT_GROUP_SYMMETRY = False
   SCF_GUESS = read
   SOLVENT_METHOD = PCM
   STS_DC = true
$end

$pcm
   THEORY                CPCM
   heavypoints           590
   method                swig
   radii                 bondi
   solver                inversion
$end

$solvent
   DIELECTRIC  7.5
   OPTICALDIELECTRIC  1.97
$end

CDFTCI

$molecule
-1 2
   C       2.68641000     -0.43326000     -3.93764000
   C       3.38058000      0.91782000     -4.20888000
   C       3.88034000      1.57322000     -2.90874000
   C       2.72404000      1.74215000     -1.90951000
   C       2.02042000      0.41030000     -1.64388000
   C       1.52629000     -0.23478000     -2.94239000
   H       3.42781000     -1.08212000     -3.43973000
   H       2.67521000      1.59934000     -4.70460000
   H       4.22598000      0.77975000     -4.89228000
   H       4.60695000      0.88516000     -2.45426000
   H       2.00089000      2.46157000     -2.31674000
   H       3.10554000      2.16857000     -0.97495000
   H       1.18068000      0.56197000     -0.95716000
   H       2.71878000     -0.27357000     -1.14247000
   H       1.04697000     -1.19576000     -2.72540000
   H       0.75978000      0.41525000     -3.38853000
   C       2.25567000     -1.10964000     -5.22643000
   C       2.84670000     -2.29619000     -5.68842000
   C       2.50041000     -2.90277000     -6.88317000
   C       1.49838000     -2.35947000     -7.75749000
   C       0.89327000     -1.15153000     -7.26645000
   C       1.26325000     -0.57238000     -6.06821000
   C       1.14280000     -2.96018000     -9.00827000
   C       1.75445000     -4.17331000     -9.49510000
   C       1.41855000     -4.73603000    -10.70929000
   C       0.44908000     -4.16064000    -11.55417000
   C      -0.17225000     -2.97871000    -11.10424000
   C       0.14944000     -2.40119000     -9.89321000
   H       3.62104000     -2.75294000     -5.07277000
   H       3.02019000     -3.81591000     -7.15817000
   H       0.11586000     -0.66244000     -7.84643000
   H       0.77260000      0.34635000     -5.75248000
   H       2.51075000     -4.67285000     -8.89666000
   H       1.92245000     -5.65094000    -11.01885000
   H       0.19003000     -4.60890000    -12.50805000
   H      -0.92947000     -2.50081000    -11.72468000
   H      -0.37179000     -1.49141000     -9.60928000
   C       3.96112000      3.93809000     -3.78835000
   C       4.59658000      2.88220000     -3.17431000
   C       5.95256000      3.04289000     -2.78334000
   C       6.62711000      4.21570000     -3.00699000
   C       5.98553000      5.31114000     -3.64104000
   C       4.62669000      5.16572000     -4.03783000
   C       3.97688000      6.25790000     -4.67557000
   C       4.64518000      7.43306000     -4.90580000
   C       5.99812000      7.57698000     -4.50946000
   C       6.65142000      6.54104000     -3.89232000
   H       2.92236000      3.84608000     -4.09783000
   H       6.45850000      2.21250000     -2.29785000
   H       7.66500000      4.31989000     -2.70211000
   H       2.93941000      6.14358000     -4.97804000
   H       4.14020000      8.26083000     -5.39386000
   H       6.51489000      8.51308000     -4.69656000
   H       7.68927000      6.64618000     -3.58755000
$end

$rem
   METHOD                    = wB97M-V
   BASIS                     = 6-311+G**
   GUI                       = 2
   SCF_MAX_CYCLES            = 800
   CDFTCI                    = TRUE
   CDFTCI_PRINT              = 2
   CDFT_THRESH               = 7
   CDFTCI_SKIP_PROMOLECULES  = TRUE
   THRESH                    = 14
   S2THRESH                  = 14
   POINT_GROUP_SYMMETRY      = FALSE
   SOLVENT_METHOD            = PCM
   MEM_TOTAL                 = 248000
   MEM_STATIC                = 4000
$end

$cdft
 1.0
 1.0  17 37
 1.0
 1.0  17 37  s
 -------------
 1.0
 1.0  38 54
 1.0
 1.0  38 54  s
$end

$pcm
   THEORY                CPCM
   HEAVYPOINTS           590
   METHOD                SWIG
   RADII                 BONDI
   SOLVER                INVERSION
$end

$solvent
   DIELECTRIC            7.5
   OPTICALDIELECTRIC     1.97
$end