Very interesting. There is a lot I hadn't considered.
That said, usually the outer layer of any material (whether it be sand, gravel, or soil) is pretty contaminated by rain, roots, and oxidisation. This is even true of some types of rocks, where the outermost layer will have oxidised. So with the exception of some rocks, having the first half block produce nothing of use for the player might be pretty immersive.
The issue with vegetation might be more difficult (requiring producing plant variants for half-height bricks)? A nuisance but doable?
Beyond that I don't see any other issues (assuming the half-blocks are just there for aesthetics and locomotion). I'm curious if you know of more (beyond those you've raised)? I'm quite curious.