This comment thread provides the initial concerns with the atom index as the bond property for TORC and RCA4.
https://github.com/ericchansen/q2mm/commit/2e9c2e98b97a0603961973ec08de487ce687d922#commitcomment-21991092

I have found that this is not only a problem for what is discussed in the commit but also after a merging of structures. For example:
Template (S1) has the substructure C2=C2-C3 with atom indices of [1, 2, 3]
Structure to merge (S2) is a ring: C2=C2-C3-C3-C3-C3-1 with atom indices [1, 4, 5, 8, 11, 14] (plus hydrogens)

If S2 has a RCA4 between atoms [14, 1, 4, 5] and is then merged onto the template the resulting RCA4 bond property of the merged structure (S3) will be listed as [14, 1, 2, 5], but atoms 14 and 15 are not S2[14] an S2[15] anymore because of the merging sequence.

It might be better to read/write the atom index, but when manipulating structures this property becomes an schrodinger.structure._structureatom object.