The problem is that Linux does not have solid way of setting environment variables for an user (or user session). .bashrc is relevant for only bash (obviously), but bash is not the only thing that needs PATH and other env vars.

At least systemd brought some sanity with environment.d, but as this thread (and jvns article) shows it's not very well known. And of course there is still all sorts of weird inherited complexity like pam_env.