#2, teleporter markers: Mark pairs with colorful shapes, or with letters. If UI professionals believe light-grey on black is easier than white on black, then use light-grey on black. What happens when the level's bg is not black? Is the bg still dark?
#3, hatch shows all permanents: I feel it's good design to display all permanents. Main reasoning: When you need the info 100 % of the time, then don't show that there is info available; instead, give the info up-front. Remove indirection.
Most hatches assign nothing. Among the permanent-assigning hatches, most assign only 1 or 2 permanents. Make these hatches look good. I hope that nobody wants to disable these 1 or 2 markings.
The rules allow 5 different permanents on a hatch, zombie is a permanent. That's an arcane corner case. It's okay if a hatch with 5 permanents looks mediocre.
-- Simon