I mean, they don't really change anything about the run itself, right?

They're not really "banned".
You could just download a mod which allows you to see DS4 buttons on your screen.
Also, I think it's not there from the beginning on because Windows/Microsoft. There are some games with DS4 button prompts, but in comparison not many games have this "feature".
And no, they don't change anything about the run itself. They're just button prompts, and if you know what you have to do anyway you could run this game without any button prompts.

There was an issue back in 2017(?) where a certain mod that changed the prompts to DS4 prompts was found to be having an impact on other areas of the game. I can't remember what exactly the issue was though since it was so long ago but if you searched in the Discord server you could probably find it.

To be extra clear, if you submit a run with the mod active the run will be rejected.

oo
Didn't knew that