After the OTA it seems the one the ROM wanted got removed, so now the -downloadable Phone version came from the Play Store again and I lost Call Screen.
Edit: Dirty flashing 0529 got it all working again even though the Dialer addon.d sh and prop entries remained the correct shorter lists.

Must be something still missing from addon.d for that transition to fewer entries/files to fail? Something which registers/activates the overlay perhaps?
Edit 2: Looking through the addon.d files only GmsCore, GooglePlayStore, GoogleServicesFramework, DevicePersonalizationServices, DigitalWellbeing, Gmail, GoogleCalendar, GoogleMaps, GoogleMessages, GooglePhotos, GoogleRecorder, GoogleTTS, PrivateComputeServices, TrichromeLibrary, and WebViewGoogle have the duplicate entries.
Of these most were actually installed to product only; Gmail, Photos and TTS were actually installed to system only; and Trichrome and WebView were actually installed to both, suggesting a problem there. system overlays contained duplicate files for most that aren't actually in system, suggesting another problem there.
I also noticed that AndroidAuto, GBoard, and GoogleClock create extra prop files in product, though they're empty, unlike their system counterparts.
I cleaned up all the entries and files manually, and have dirty flashed directly after to keep things working, and I went with the default product location for the complete duplicate Trichrome and WebView files.