It would be great if the popover were transparent so I could see which note I’m on when entering guitar fingerings.
Good point.
PFA, I assume?
The orange note is the one you’re on, surely?
And the answer is “4” - sorry, couldn’t resist… 
Things can be similarly dicey for entering lyrics on long melismas of short notes. It’s very easy to lose track of where you are in the melisma requiring trial and correction. I hope they will refine the way this works and either highlight the effected note or add a connector line Between the note and pop up (or something else) in the future.
Lyrics entry doesn’t behave the same way as fingering entry, and probably should.
Fingering entry clearly highlights the note to be affected.
There are situations where it’s very useful for lyrics to not be attached to notes (or to be attached midway through tied notes), just as there are situations where it’s useful for playing techniques to be attached to rhythmic positions midway through notes. I’d rather the existing functionality didn’t change.
Good point about lyrics.
Have I misunderstood the OP somehow?