Why not? I'm running vanilla AOSP with F-Droid apps only. No Google Apps framework.
Threats are limited then to regular baseband radio issues. I know I could be doing better if we had open hardware, but that's the most practical solution I can implement today I think.
Have you considered writing a guide on how you do this and what changes you make? I also own a Pixel, but kept running into problems when I tried to compile Android, eventually making me give up.
It's doesn't resolve the tracking issues.