> X11's practical absence of any security mechanisms for user sessions means you should probably not run any kind of low-trust UI program

This has nothing to do with X11 or even UI at all. You should not run any low-trust program whatsoever (outside of a container). Any program that runs as your user can change your ~/.bashrc or any other file on your homedir.

Of course this is a feature that you want, for example when you edit these files with a text editor.