I think that the first thing that came in Stan and Jack's minds is that it's nice to draw people with cool super-powers, it looks good on paper. I remember reading that they didn't want to be bothered with the origins of their super-heroes, so they say they were born like that. These creatures, born different, shouldn't they suffer from the discrimination of the rest of the population? Sounds logical… It has been present from the start but not present all of the time and it has been fluctuating depending on the author and the stories he wanted to tell. X-men is a material, the discrimination subject can be picked but eventually, it's between an author and his obsessions (like Hickman only keeps some aspects of the X-men and leaves others). I haven't read all the X-men comics but the ones I read, this subject hadn't been that compulsive like now.
I'm sure that if today's authors had more imagination (or freedom), they could come with others stories, other subjects to explore. The way they "shout at the top of their lungs" all the time is quite boring and is the path to a atmosphere that is poisonous and please only those who like to see extreme solutions implemented in a world that can sustain them since it's only imaginary and it has no painful consequences.