I have recently been experimenting with the different ways to run things at startup/logon, and I have found something that I don't quite understand.
Autoruns treats entries in HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Run as things that will run at logon.
However, you can go to the Settings GUI, go to Startup apps, and disable them there, but they will not disappear (or get moved) from the registry.
Meanwhile, if you disable them through Autoruns, they simply are moved to a subkey named AutorunsDisabled (and they disappear from the settings startup apps list), so it seems like the registry entries are simply a list of POTENTIAL startup commands, and there should be something somewhere that enables or disables those.
Since I'm trying to learn how these work so I can add or remove them programmatically, What does the Settings GUI do under the hood to let the computer know which entries to run and which entries to ignore?