Forgot to add that I tried using the SecItemCopyMatching function to read the certificates from the iOS Keychain, but I haven't been able to get this to see the *.pfx certificate under "Configuration Profile".

I still see this happening with iOS 15 simulator. This answer on Stack Overflow, to add a frame with minimum sizes for the popover, seems to help: https://stackoverflow.com/a/64253444/1359088

I'm answering this way late, but what about a BackgroundTask? These will definitely run even if the device is locked and turned off, as long as the app is running. The only bad thing is you don't get to choose when it runs; the device decides when to run. However, they seem to run pretty quickly after locking the device, from my experience, and you can have the task schedule another task when it's done, so they can keep being scheduled repeatedly. https://developer.apple.com/documentation/backgroundtasks