So this caused me to go digging as I've run into the same issue. Make sure it's up to date first obviously, and if it still refuses to function, their page has fixes which ended working for me:
Have you updated recently? A few weeks ago there were some changes to YouTube that basically shut down newpipe and other similar clients, but an update should have fixed that.
PipePipe from f-droid is a clone that seems to update more frequently than newpipe, and has the additional benefit of being able to access the Chinese and Japanese video sites bilibili and niconico (worth checking out, it's fascinating even for someone who doesn't speak the languages)
Far as I can tell, that's the one I get when opening in Firefox and then switching to desktop mode.
Everything except geo-blocked vids works perfectly now that I have NewPipe set as the default app for all YouTube links, though, are you sure yours is updated?
I use the same setup as you, opening all YouTube links in the app. I just checked again, I have the latest fdroid version which is 3 weeks old and the issue persists, also did a reinstall for good measure.
I also have the tubular fork installed from the latest apk, and it has the exact same issue.
I also tried from different locations via VPN but nothing helps :/