I made 2 alternative Touch Bar layouts one for Cinema4D and one for Lightroom.
After the update to 3.0 and so on my "Lightroom" Touch Bar setup is not working Cinema4D is showing.
This should still be working fine. Maybe it's just hidden (unhide via predefined action "Toggle BetterTouchTool Touch Bar") or you have accidentally overriden the app specific Touch Bar behavior?
Unfortunately that doesn't workout for me.
All other apps the TouchBar Layout shows up, the one from Lightroom not.
Tried every option in the Touch Bar Configuration dropdown menu, did a restart of BTT.