I use SwiftKey and this is the first I've heard of FPS interference. My FPS works fine and I wouldn't want to give up my SwiftKey.
I'm using Pixel 2 XL, which model are you using?
If you reinstall SwiftKey, does your FPS then go away again?
Because I am the first one to figure this out going by the LACK of useful help found via Google.
I used SwiftKey on the Pixel XL (Pixel 1) with Oreo and Pie with NO issues.
I now have, yes -- the Pixel 2 XL -- just it bought Thursday. Un-boxed it and the FP reader was just fine, running Oreo.
Patched to Pie AND -- installed SwiftKey along with my apps. Bam. Stopped working reliably. Would get "Fingerprint Reader Hardware Unavailable" VERY very often.
Did numerous wipes, delete FP's, re-enroll. The pattern was after each wipe, the reader would work 100% until I placed my apps back.
Then yesterday after booting to safe mode and back I had it working well -- again. The it hit me. Safe Mode reverts the keyboard back each time to Gboard. And of course each time I would re-enable SwiftKey. And the issues would return.
I mean, I was having it work only about probably 30% of the time, and I use my phone heavily. Since dumping SwiftKey, the FPR has worked 100%.
Google says 3rd party apps can be the source of FP reader issues, and you can bet the keyboard app is the most likely culprit due to it and the FP reader both interacting with the OS at the same points (ie the device auth/unlock attempts).
Of course there might be some other device specific factor involved. Evidently there is, since you have no issues. Who knows -- but anyone having FPR issues and using SwiftKey should probably try its removal.