There is a lot of articles to be found here covering various sides of your question.
You cannot control where the applications install to and you should not mess with permissions on system folder structures. You may cause irreparable problems.
Create your own dedicated structure - if you - as I do - hate long paths - you can shorten your names - just be consistent.
I am a developer and a breaker - I break my systems to learn their limits - at the same time I am deeply addicted to be able to use my computer - so long time ago I developed my own routines.
I keep all my stuff - on separate partitions on separate devices.
I have shared the idea , the principles behind.
And some required low-level setup
I have also shared what I call common pitfalls for a developer on Arch based systems
Utility scripts
I could have shared the complete setup - but then, where’s the readers learning process - and I would only put myself in a position where I have to explain my logic instead of the reader creating his/her own logic.