Reporting homozygous reference is important as it distinguishes that position from a no call position.

To answer the question: do samples A and B have the same alleles at position X, you need to know what the alleles are in both samples. If your SNV caller is unable to call position X in one of the samples (e.g. insufficient enough coverage, read mapqs too low, ...), then the answer to that question is "I don't know".This is not the same as "hom ref in both" and "ref in one, non-ref in other" and these cases need to be treated differently.