It just so happens I very recently received vroptician comfort prescription lenses. I did some testing with both inserts, no inserts, and only one lens and forcing steamvr to track only one eye. As far as I can tell they do not hinder eye tracking. In my case I did not notice the foveation area flick to bottom when blinking you mentioned.
It's a bit too soon to say for sure, I need to spend some more time with it. In any case, nothing egregious out of the box.
Update: I forgot to mention I still use the spacer because I could feel my eyebrows pressing on the top of the lenses when I removed it. Might be a factor or not at all.