The why's really depend on the group but most just simply are looking for like minded people that fit them and what they do. That's the simple "why".
My best advice: treat not a small number of raiding guilds as cliques/frats/exclusive groups. They, whether you like it or not or agree or not, have hoops(standards) they expect others to jump through.
If they don't know you before you join(ie you didnt get in based off of knowing someone who slides you in) they're going to use basic tools to discern whether you fit what they do or not.
Obviously, one of those would be a screen of your UI.
Another way to look at it is that you're a rookie looking to join their team. The onus is on you to fit in with them, not for them to go out of their perceived way to accommodate you. To them UI's/addons are tools to many of them that reflect you are being an asset(whether you think so or not). Perhaps even some of them don't actually use all they guild's standards expect to get in with. But they're not needing to prove themselves any more as as a plebe is expected to do.
To be clear, Im not condoning groups that use those standards as a black and white way to determine someone who can be an asset to their guild. I think it is a recipe of things that determines who can do well, personally. But I also have been in guilds that for them, perception is everything and they dont have the time/desire to develop people to raid with them, preferring instead to just go with people they perceive to be able to hit the ground running(whether true or not).
So you've a few options:
1. Do a screenie of the UI they want(ie by seeing other apps/talking with others in already) and not use said UI actually when you're in the group(once in they're most likely not going to be carding you on your ui over and over).
2. Network yourself with those who make yay or nay decisions and circumvent that.
3. Try to learn to use the UI/addons/bells and whistles that they expect of you. In the short run it may be troublesome but there may be potential for it to improve what you do. Yes, you may do better/be better without such but then again you may improve what you do by slight or significant amounts too. You dont know until you give it a try.
In the end it really just will depend on how much you want to be apart of what those groups do.