People mod for all sorts of reasons other than to make things "more real". They mod tails so that people can play as whatever animal race they want. They mod outfits to fit their particular taste in clothing and apparel design. They mod weapons because there are particular things about a weapon they'd like changed.

The other thing is, I consider there to be a large difference between telling someone "It's just pixels" when they're actually afraid of their character being seen naked, and telling someone "It's just pixels" when they take a mod to "dye" something that in game is undyeable.
My point was that people do it because is it important for them in one way or another so at the end of the day is more "than just pixels". I can't for the life of my play Skyrim without modding, I need my character looking in a certain way or I will enjoy the game less (now you also know why I don't agree with "is just cosmetics").

Anyway, I understand your point, but to me, the problem is the OP caring for something her/him don't have any control over it and not "just pixels".