While investigating Startup Applications, I noticed one named "Program". Using Task Manager, I was able to add "Command line" column under the Startup tab. This showed me which application was being started. In my case, it was WinHotKey. Also, "Startup type" column, to expose where the startup configuration lives (ie: Registry).
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run
Place double quotes around the value. For example:
"C:\Program Files (x86)\WinHotKey\WinHotKey.exe"
Seems like this is also true for many other applications, such as Docker Desktop, and appears to be an uncaught Windows 11 regression. The only applications that place double quotes by default are those developed by Microsoft.