As I reply everyone raising this "bug", get a properly configured sudo. Even though I don't recommend using Geany as root, I can just fine run sudo geany on my Debian machine and it works flawlessly (as far as I can tell without doing it daily, though), whether or not I have other Geanys running. It properly uses /root/.config/geany as the configuration directory.

Anything that would lead to another user (including root) to writing in a user's home directory should be avoided. If you did write there as root, the user would be left with root-owned file in his home, files he couldn't modify. That's not a good thing.

And while I don't want special code for handling sudo use, I don't think any is needed: proof being I can use sudo just fine on my machine. Yes, Debian does have Defaults env_reset.

If you really want us to change something, you'll need to detail why you'd need inheriting the environment (including HOME and XDG_*, and possibly other) in your sudo session, and what you'd want us to do to fix it (by that I mean actual changes, not "fix it").

If "many other GUI tools" work, it might be for a number of reasons, one possibly being that they use DBus (anything using dconf comes to mind), which may or may not use $USER rather than $HOME/$XDG_*. Or other special handling. Or possibly simply not have to do any IPC and happily mess up your user's home directory.
If really other tools to something meaningful and it's not a hack, maybe it could be a basis for proposing a change.

Out of curiosity, do you have root-owned stuff in your dotfiles? (cd && find -path './.*' -user root)

I'm not closing it just now, but I still do consider this invalid at least for the moment

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