Yeah, I'm pretty sure it's just something to do with DOSBox. To my knowledge there's no difference between the two versions, although U4 is such a small game that you could install both and check for yourself and not really have to worry about wasting any space worth thinking about.
The "different" versions of Ultima IV are actually console versions, which you won't find here on GOG. There's a Sega Master System version, which is a straight port with graphics improvements, though I think only Europe officially got it (not that this would stop you from emulating if that's your thing). Gameplay-wise the differences are dungeons (which are top-down instead of overhead like on PC) and dialogue (you choose keywords from a list rather than typing them, and the game reveals new keywords for you as you go through convos).
There's also a Nintendo Entertainment System port which seems to be the same as the Master System version except with graphics heavily overhauled to be very chibi-style and JRPGish to appeal to Japanese gamers. Probably not the one to play unless you particularly like that aesthetic.
EDIT: There are also a couple of unofficial rebuilds of U4 floating around online, I think, but I don't know much about them besides them having a few graphics tweaks and being made to run on modern systems.
Actually, about the console ports:
The dungeons are still first-person in both ports.
The SMS version is pretty faithful to the original. Dialogue uses a keyword system. (One annoying thing: you can't just go around asking everyone about "rune" or "mantra"; you have to learn who to ask through dialogue,) Ranged weapons can fire in all directions, but can't go through walls and some have limited range. Mixing spells works either like the original or Ultima V (I forgot which).
The NES version is completely different. The battle mechanics have been completely redone. Characters can equip both a bow and another weapon at the same time. Ranged weapons can fire in all directions, have infinite range, and can fire through walls. Mixing spells is more like Ultima VI; if you know a spell and have the reagents (called "herbs" in the English translation), you can cast it without mixing before hand. You do, however, have to learn certain spells before you can cast them. The spell list also changed. Reagent costs are the same at every store, unlike other versions.
In the NES version, there are fewer distinct dungeon rooms. Many rooms are repeated. The Abyss, in particular, is much simpler, but only the Avatar can go in. Speaking of which, the Avatar now gets 99 MP regardless of class. On the other hand, you only get one of each Exotic equipment and can't sell it for lots of money. There are a few new items, such as the Flute that a Shepherd (only) can use once per day to put all enemies to sleep. Keys are much more expensive, but you only need 1, as it has infinte uses.
The NES version lacks food. Resting and saving is only possible at inns. Also, party size is limited to 4 characters; everyone else waits in Castle Britannia. You can't buy any horses because they're all dead.
I mentioned the "English translation" earlier; that's because the NES version was translated from Japanese, which in turn was translated from English. Needless to say, things were lost in double translation.
There was also a version for the MSX computer, which I believe was based on the NES version.