Brake cable rubbing seat post
I think that letting the (inner) cables rub against the seat post is a bad idea. It will cause wear on the cable, scratch your seat post (or seat tube) and probably create noise every time you hit a bump.

Why not go for your third option? Put a cable stop before and after the seat post and run a short length of (almost straight) cable housing around it. Works fine on normal bikes as well, after all.

The first option (continuous cable housing) causes squishy braking, even on normal bikes with shorter cables.

Can’t you run the shifter cable in a straight line along the bottom tube?

I wouldn’t run the cables on the side of the top tube, it causes problems when you lean the bike against something.