1. You can’t easily define what apps start with startup

For point 2, that is true and improving. Always do some research about program compatibility before completely changing your computer's OS.

For point 3. Programs are generally installed in /usr/bin and ~/.var/app for Flatpaks (analogous to MS Store). Much easier than finding where MS store apps are installed.

Never come across point 4, so I can't dismiss it.

5. As with 2, depends on your usecase

6. GNOME Disk manager (comes with Fedora and Ubuntu) has options to mount drives to arbitrary locations if needed.

I understand your argument but making points like these don't really contribute to the discussion.