I keep long hives (horizontal langs) but have been rearing for fast splits, not honey surplus, so I haven't bothered to super them yet. So this $0.02 is mostly speculative.
If you only have an entrance at one end of your hive, it would seem to make sense to super up under it rather than make the foragers or the storage bees make the long walk to the other end of the hive. I don't see any reason why you couldn't shim between the bottom box and the super, or move the entrance up with the super, or both...
People keeping in vertical Langstroths sometimes advocate having a top entrance over the supers so that foragers go directly in to the super. A quick search of the forum will also yield endless debates about whether swarming bees choosing an optimum location prefer top, bottom, or middle entrances, which might help inform your decision.
Me, I doubt any increase in efficiency makes that much difference. Just make sure your entrance(s) is large enough to allow full forager traffic, that you have a method for reducing it in case of robbing, and that it is located somewhere that mortuary bees can reach pulling out the dead.
(That might be one argument against having only one entrance up on the top of the super stack. Mortuary bees can climb just fine with their burdens, but do you want them to have to climb all the way to the top for each trip?)