"Startup Applications" should have reversability: always allow any removed app to be restored.
"Startup Applications" tab allows you to remove apps, but not every app removed can be easily added back.
For example, in Debian GNU/Linux right now (up-to-date 'testing' distro with Gnome Shell 3.30.0), the only two Startup Applications listed by default are "SSH Key Agent" and "GPG Password Agent". If you remove the SSH one, and then change your mind, there's no way to add it back. When you click on the "+" bar, it's not listed as one of the offered apps (for that matter, neither is "GPG Password Agent").
Maybe removed applications could get moved into ~/.config/autostart/removed/
or something, and gnome-tweaks
would know to look for archived app-launch scripts there so that it could always include them in the list of apps to offer.
(See also somewhat-related issue #42 (closed).)