I was thinking that it would be cool to have a projected rails directly above normal rails, but it seems like I cannot place them like that. They become diagonal, break when there are more than 2 placed, curve etc. Just weird behavior. Try for yourself to see what I mean.

• Here a screencast of how the carts snap weirldy
• Here how weird placing them is and that it's not intuitive

I also wonder, if maybe wouldn't it be better to have projected rails in the air have hitboxes (so that we can step on them)?

There's no easy way around this. It's not worth the trouble to fix.
Hologram rails having no collision is the entire point.