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In most of society cousins marriage [..]
Who cares about marriage in biology? We only care about reproduction. Marriage is a social construct that is mainly irrelevant here.
[..] is seen bad due to fear of bad genes
The term "bad" is poorly used for 2 reasons. 1. There are no bad genes but only a selective differential between two alleles of this gene (or at any other sequence for that matter). 2. It relationship of dominance and epistasis that causes inbreeding depression and not bad alleles.
I have "X" and "X" chromosome, X came from my father and X from mother son of my mothers brother will have Y chromosome and X from his mother which is not family and since my mother has nothing to do with "Y" chromosome.
That's one long sentence :) Who is "mother son of my mothers brother"? You might have a typo here.
Why do you talk only about "X | Y" chromosomes? "X | Y" is one of the 23 pairs of chromosomes we have (not mentioning mtDNA).
Does this all mean that this marriage is as good as between unrelated people?
The whole question is to know whether the two parents are related (in biological terms). What I mean by related is not is they know each or if their respective siblings got a baby together but if they share a common grandmother for example. If you draw the genealogical tree of each parent and you see a recent shared ancestor between the two parents, then inbreeding depression can be an issue. Otherwise, it is fine. The reproduction events occurring between their respective siblings is irrelevant.
However, be careful if you intend to jump into societal consequence. Science will not tell you what is acceptable or not in a society. It won't tell you what is good and what is bad. Knowing that a couple have no risk of inbreeding depression may affect your view about this couple but it does not mean that science has demonstrated that the marriage should or should not be allowed (assuming the society has anything to say on that matter).