I'm using Android 10, which has a global setting for a dark theme. Expected behaviour for this is that if I've selected dark mode in the OS, it should filter down to individual apps, too.

I was unaware that andOTP had a dark theme, but pleased to have discovered it. You may wish to check the below article for a few ideas on how to implement this feature in an Android 10 compatible way.

“Implementing Dark Theme in your Android app” by Frank https://medium.com/q42-engineering/android-dark-theme-b4d695f78c4f