I've never had this problem on Manjaro Phosh and also not on Mobian when I last used it a couple of months ago. The call window was always on top of the lockscreen. But anyway the release notes of Phosh 0.13 mention the ability to handle incoming calls on the lockscreen as a new feature, so it sounds like the problem would be solved once that update lands in Mobian.
Edit: Just tested it with Phosh 0.13, the incoming call is now indeed integrated in the lockscreen rather than being an overlay window.
Edit: Just tested it with Phosh 0.13, the incoming call is now indeed integrated in the lockscreen rather than being an overlay window.