Not recognising family since 3.12 update

Describe the bug
The reaction [O]C(=C=O)C=O + C1CO1 <=> O=C=C(O)C=O + [CH]1CO1 was originally identified as an H Abstraction reaction in ARC 3.7

However, since moving to 3.12 and disconnecting from RMG - it is now not recognised with any family if one includes the XYZs in the species when creating an ARCReaction.

allow_nonisomorphic_2d: true
compute_thermo: false
job_types:
  fine: true
  freq: true
  irc: false
  opt: true
  rotors: true
  sp: true
opt_level:
  method: wb97xd
  basis: def2tzvp
freq_level:
  method: wb97xd
  basis: def2tzvp
scan_level:
  method: wb97xd
  basis: def2tzvp
sp_level:
  method: DLPNO-CCSD(T)-F12
  basis: cc-pVTZ-F12
  auxiliary_basis: aug-cc-pVTZ/C cc-pVTZ-F12-CABS
project: rxn_10218
reactions:
- label: _O_C(=C=O)C=O + C1CO1 <=> O=C=C(O)C=O + _CH_1CO1
skip_nmd: true
species:
- label: _O_C(=C=O)C=O
  smiles: '[O]C(=C=O)C=O'
- label: C1CO1
  smiles: C1CO1
- label: O=C=C(O)C=O
  smiles: O=C=C(O)C=O
- label: _CH_1CO1
  smiles: '[CH]1CO1'

R1H
C1CO1
C       0.09620000   -0.66860000    0.44160000
C       0.03240000   -0.04470000   -0.86630000
O      -0.15040000    0.67160000    0.38390000
H       1.11070000   -0.85450000    0.78800000
H      -0.62170000   -1.32840000    0.92420000
H       0.96080000    0.17890000   -1.37800000
H      -0.87000000   -0.11020000   -1.46390000

R2H
O=C[C-](O)C#[O+]
O      -0.43500000   -1.52130000   -0.12000000
C      -0.04380000   -0.25230000    0.01860000
C      -0.02540000    0.28510000    1.25510000
O       0.02630000    0.73050000    2.30950000
C       0.33380000    0.62050000   -1.08760000
O       0.26190000    0.29560000   -2.24710000
H       0.69020000    1.62670000   -0.78840000
H      -1.33680000   -1.54280000   -0.44860000

R2
O=[C]C(=O)C=O
O       0.29570000    1.77440000   -0.26520000
C       0.17750000    0.55090000   -0.06550000
C       1.31330000   -0.20160000    0.29380000
O       2.28190000   -0.72480000    0.57870000
C      -1.05990000   -0.26830000   -0.15870000
O      -1.05780000   -1.45280000    0.05740000
H      -1.96320000    0.30070000   -0.43910000

R1
[CH]1CO1
C       0.82440000   -0.23630000   -0.27650000
C      -0.57340000    0.04920000   -0.06040000
O       0.26950000   -0.66510000    0.88320000
H       1.70870000    0.39350000   -0.29280000
H      -0.90430000    1.02050000    0.29510000
H      -1.32490000   -0.56180000   -0.54860000

Start by reproducing ARCReaction creation with the provided YAML, species, XYZ data, and reaction, then compare family recognition between ARC 3.7 and 3.12. The fix is complete when this reaction is recognized as an H Abstraction family while the species include their XYZs.