fix(python/fmt/cif): pass internal reference to subobject and support inconsistent CIF files

[jnooree]

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[codecov]

Codecov Report

Attention: Patch coverage is 85.29412% with 5 lines in your changes missing coverage. Please review.

Project coverage is 91.15%. Comparing base (81f797b) to head (b7e504e).
Report is 6 commits behind head on main.

Files with missing lines	Patch %	Lines
python/src/nuri/fmt/cif.cpp	84.37%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #447      +/-   ##
==========================================
- Coverage   91.18%   91.15%   -0.03%     
==========================================
  Files          58       58              
  Lines       13477    13484       +7     
==========================================
+ Hits        12289    12292       +3     
- Misses       1188     1192       +4     

Files with missing lines	Coverage Δ
python/include/nuri/python/utils.h	97.93% <100.00%> (+0.01%)	⬆️
python/src/nuri/fmt/cif.cpp	92.10% <84.37%> (-2.42%)	⬇️