Here's an example of where the skype app startup info is in the registry. The registry keiy name "SkypeStarup" is completely arbitrary and is set in the appx manifest in a taskid attribute. "1" disables the startup of the app. These startups can't be detected by Sysinternals Autoruns, but they are in the Settings app. The apps framework is sloppily designed, and hard to manage,.
HKCU\Software\Classes\Local Settings\Software\Microsoft\Windows\CurrentVersion\AppModel\SystemAppData\Microsoft.SkypeApp_kzf8qxf38zg5c\SkypeStartup\State=1(dword) (from procmon category is write)
See also the other place you posted your question: https://stackoverflow.com/questions/63746294/how-to-use-powershell-to-manage-startup-items-of-uwp-app-in-windwos-10/