It'll come down to the skill of the designer, at days end, to see how well they're used. Personally I don't think I'd ever mix the two in a single level, unless I was going to give a sort of extra upgrade to make the difference, like how 'Teenhmifnoeafgil' (if I spelled that right I should have a prize) gives an upgrade before you can start jumping.
I was thinking Ego, the overlay is extraordinarily useful, opening myriad possibilities in the mod level I'm working on despite me only being 4 screens into the second environment, but at times it'd be nice to be able to overlay the background but not Juni. Like where I want to partially mask a waterfall with a bit of background wall, but I don't want Juni to disappear behind that scrap of wall if the player jumps that way. Is it possible to get a second type of overlay that doesn't cover Juni?
Sorry; I know you're getting a ton of small requests and then second types of those requests... But it's a thought and it'd be handy. At the moment I'm having to shape my backgrounds to work around it. I could always make a CO but the overlay is made to make that less necessary.