The weird thing is that -Q -u [user] loads an init file at all. I'd call that a bug, but it's probably been this way for decades.
Given that it does, I suspect there's no difference between these:
emacs -q -u "$USER"
I.e. you've reverted the --no-init-file (aka -q) behaviour by specifying an init file (although again, I find that surprising)...
You probably want to start with desktop-save-mode.
There are parts to your question which I have not addressed.
starting emacs automatically on boot, this is usually OS specific
opening recently used files
With desktop-save-mode, unless something bad happens, restarting emacs will bring you back to exactly where you were including registers, tab/window ...