IIRC I had to keep xsettingsd running in the background for my system GTK theme to be applied to Flatpak apps so maybe that’s what you need?

I’ve tried both and ~/.local/bin tends to be used by a bunch of tools to install their own binaries/scripts so depending on what you use it can become very messy (which did happen in my case). I used to have a ~/Documents/Scripts directory in my $PATH and that was much cleaner than my current setup so that’s what I’d recommend, especially if you want to use Git with it! :)

Sometimes it’s plug-n-play and everything works great. Sometimes you press the update Nvidia drivers button on your Ubuntu work computer and then need to tell IT you bricked your OS. YMMV