Because of the possibility of inverted gravity being added in the future. It's a slim chance, but not conclusively ruled out. If we were to allow inverted entrances now, we'd either have to:
a) have "spawns upside down lemmings" as a separate flag (and in the past, we did have "Flip graphic horizontally" and "Flip lemming direction" as separate flags, and it was decided to merge these)
b) break all levels currently using inverted entrances
c) cancel the upside-down for all levels predating the feature - which would in turn require a way to distinguish, which in turn is basically just a way of implementing then immediately culling option A
If you want to have your lemmings come out of the ground, my suggestion is to design a new entrance object that suits such a visual effect.
On the flipside (pun not intended, but very much enjoyed when I spotted it), for an exit, the only thing that might need to change is the trigger area. Even this could be addressed with a "trigger area vertical offset doesn't apply to invert-gravity lemmings" type rule.
