The problem isn't you. It's the way Unix-inspired systems do things that are entirely wrong. It's an insane mess of all of the things you mentioned because all the programs could do whatever they wanted. Bad conventions emerged and were propagated throughout the ecosystem.
Here's a fun exercise: try to change your home directory's physical location on a *nix system and see if anything works afterwards. It won't because every config thinks your files are in /home/me while you've changed your user name/home directory to /home/new-me. Windows (eventually) actually got this (approximately) right with a 'virtual directory' for 'my home directory' regardless of where exactly it is on disk. Programs refer to that virtual location.
The current status quo on any *nix is absurd.
(Just FTR, I only use Linux systems, personally. My criticism is borne from a place of aspiration/hope.)
Yeah I've never really had a problem either. Even with using skels.
Besides, install scripts are the norm for me, so it's typically easy to fix when things do go wrong.
Pro tip: "${HOME%/}/" will always result in /home/godelski even if I include my last name and even if I accidentally modified it to have a / at the end. Some simply variable substitutions go a long way.
The problem isn't you. It's the way Unix-inspired systems do things that are entirely wrong. It's an insane mess of all of the things you mentioned because all the programs could do whatever they wanted. Bad conventions emerged and were propagated throughout the ecosystem.
Here's a fun exercise: try to change your home directory's physical location on a *nix system and see if anything works afterwards. It won't because every config thinks your files are in /home/me while you've changed your user name/home directory to /home/new-me. Windows (eventually) actually got this (approximately) right with a 'virtual directory' for 'my home directory' regardless of where exactly it is on disk. Programs refer to that virtual location.
The current status quo on any *nix is absurd.
(Just FTR, I only use Linux systems, personally. My criticism is borne from a place of aspiration/hope.)