How is it confusing?
It's the frametime, not FPS.
1000ms / frametime = FPS:
Final Fantasy: 1000ms / 34.2468ms = 29.1998084493 [Hz] ~ 29 FPS Fraps [but far more accurate]
Cube Creator: 1000ms / 99.5142ms = 10.0488171537 [Hz] ~ 10 FPS Fraps [again, far more accurate]
For reasons why developers should prefer this:
https://www.mvps.org/directx/articles/fps_versus_frame_time.htm
Note that Citra is not a benchmarking suite either, so comparing FPS is pretty useless. Instead you should state away you are from required frametimes.
Furthermore the whole FPS-to-measure-playability is also broken by design.
For turn based games 3 FPS are easily enough, for other games 20 FPS are enough etc.
Some people might even want to play fast paced games at 10 FPS, others think it's okay at 50 FPS etc.
Wether audio is messed up also depends on other factors so really there is no point in asking for a better FPS counter in Citra.
People should just trying to play their game on their hardware: either it's fast enough for them or it isn't - unless they are developers they can't change much about it anyway (and then they'd care about frametime to guess wether optimizing is enough to make things work).
What matters is perception, not some stupid number.