I suspect it’s an artistic/design decision to leave the overlay active when paused - many skins seem do this, (including Refocus, which is what I use) and some don’t. I’m not involved in the creation of the OSMC skin and don’t use it myself so this is just speculation on my part.
You’re free to use a skin which doesn’t leave the overlay up, of course. The reason why there are many skins available for Kodi is because not everybody has the same artistic tastes or functional needs from a skin, and no one skin will suit everyone.
You prefer pause to not show an overlay but if that was changed there would probably be just as many people who wanted it back the way it was. A lot of people were critical of the first incarnation of the OSMC skin, particularly the huge fonts, when a major redesign was done to address that just as many people complained about the new design and wanted it back to how it was before - it’s hard to win sometimes.
For some things you could add a preference setting in the skin but if you go too far in that direction you have dozens of preferences settings and a big unmaintainable mess.
At its core I think the OSMC skin strives to be a very clean, minimalistic, non-resource hogging skin, and that includes not having dozens of configuration options, unlike some of the more powerful but complex skins. Not everyone will like it, but you’re not forced to use it either. I choose not to use it and so can you.