Not at all, thanks for the interest and for raising these things.
Indeed, OMXPlayer was launched to accommodate users who don't need overlays on top of videos and want to have an overall better performing experience on the Pi.
Alas, it does have those known limitations, which is unfortunate and will definitely not be especially compatible with some themes.
It's not ideal, but... baby steps. We'll get there!
Thanks for the note, and keep up the good work.