I'm not sure about that. The way AlphaFold works involves transforming the protein from a vector space representing the sequence to a different vector space representing the folded structure and back again as it performs iterative refinement. Presumably you could perform a comparison in the structure space to find homologs that have completely different sequences - they would just have a high cosine similarity.

Checking sub-regions of the structure would be more difficult, but depending on how the structural representation works it could just be computationally intensive.