For me it's just SwipePad that I use which has an always on overlay. If you know what apps are overlaying I've found a workaround you can setup. Ideally an app shouldn't have an invisible overlay permanently hogging resources so you should find and disable them permanently if they're unwanted anyway. An app like Elixir with it's "running" processes/services filtered to User can help finding the culprit.
So I use a workaround to quickly disable an overlay for permission toggling. A "
Task Shortcut" that uses the Tasker Greenify plugin (don't know if pro is required) to Hibernate the overlay app/s, Wait for a configured time and then Wake. Note that the wake process takes five seconds to finish.
I open my shortcut from SwipePad itself for it to disable for ten seconds while I click away at permissions to my hearts content. When the time is up it resumes working normally and all is well :highfive: