If you need the fingerprint functionality in Apps which refuse to work with it now, and if Fairphone can’t somehow come up with something to counter Google’s requirements, then it seems currently you would indeed be left with custom ROMs which don’t adopt Google’s requirements, like LineageOS.
It’s important to note that security-aware Apps (especially banking Apps) might not like running on custom ROMs by default, so some consideration is needed with this approach, too.
The closest to a Google certified stock OS in my view should be LineageOS + Google Apps and services (via installer projects like MindTheGapps) + Google’s device registration for the use of Google Apps and services on non-certified Android OSes (https://www.google.com/android/uncertified/ to play it safe with one’s own Google account).