I don’t think it matters what genes are suppressed in humans with Y chromosomes and humans without Y chromosomes.
If Janet and John are siblings, then Janet may have genes ABCDef and John may have genes aCEgHI, where lower case are inactive, but they still share 50% of the same genes. Their offspring will have a 50% chance of sharing each of genes Aa, Cc, and Ee; their daughters will have A and/or C active, and their sons will have C and E active, but there’s still going to be a boosted chance of bad reinforcements.
The fact that gene e isn’t active in Janet doesn’t mean that it’s not still present in her gametes, and still potentially able to mess up her sons if it’s a bad recessive.
You seem to be thinking in terms of epigenetics and development, where genes can be suppressed. But for reproduction, genetics is crucial, and genetically those genes are still present; making them inactive doesn’t delete them. And because of that, if you’re deciding whether to mate with someone, the genes that are inactive still figure into the degree of relatedness.