>Will top entrances promote more comb staining?
If they keep coming in the top and you keep adding empty supers to the top where is all the traffic? Just the ones headed to the brood nest but not the ones putting honey on. If you put supers on the top and the bees are coming in the bottom every trip to store more in the supers has to cross all the capped comb to get to the supers at the top that aren't drawn yet. I don't see that there is any difference.
The main issue for color and toughness has to do with time. If the bees get time they paint the wax with some secretion that turns it yellow and makes it tough. For comb honey you don't want that to happen, so they need to build it all quickly and you need to pull it quickly.
Yeah, like MB said; You have to be ready to pull them asap when capped. All my hives have top entrances and all we do is collect "comb" honey.