Following up for anyone who finds this in a search, this was originally included in my topic of "Downward shift of home screen", but I think it's separate than just a graphics offset.
There is a bug somewhere regarding Gesture Navigation on Pixel 6a. I've found reports that other users on Android 13 (not GrapheneOS) are experiencing a freeze of the home screen gestures. Namely, you lose the ability to use the home gestures to go to "Home" or to swipe further to see Recent Apps.
The issue persists until you either (a) reboot the device, or (b) change System Navigation from Gesture to 3-Button and then back again. So it's usable if you just toggle between the 2 methods, or just leave it on 3-Button navigation.
I've tried alternate launchers and browsers to see if it might be an app-based issue .. but have found no correlation in that regard. My suspicion is that it relates to the "At A Glance" features in the Pixel Launcher which are (thankfully) not included in GrapheneOS. These features adjust the graphics down, and make for a shift in the finger print graphic away from where the sensor actually is. A shift in graphics / sensing not tied to a hardware item (home bar) off the bottom of the screen could generate this type of behavior.
I shall soldier on with the phone in 3 button navigation territory like it's 2012, and update this as the software is updated.