I haven't seen the inside of a Revell "Beagle" box in many years, but I think I remember some parts of it, at least, fairly clearly. And I got thoroughly acquainted with the Revell Bounty kit when I was working on my little model based on it ( http://www.hmsvictoryscalemodels.be/JohnTilleyBounty/index.html ).
I'm pretty sure the hulls of the two kits are identical. The quarter badges (including the windows) of the Bounty consist of separate parts that are to be cemented to the hull halves, with the aid of tiny locater pins (which the "Beagle" hull also has). The transoms are different, and the figurehead got changed from the Bounty's "woman in a riding habit" to a simple billet head.
The decks of the two kits, as I remember, are quite a bit different. The "Beagle" has an oddly-shaped part that incorporates "bulwarks" for the forward part of the ship. (The Bounty only had bulwarks around her quarterdeck.) The Revell designers, for some reason, added a pair of completely spurious chest-high pinrails to the sides of the Bounty abreast of the foremast. The instructions for the "Beagle" tell the modeler to slice them off, thereby making room for the "bulwarks" that are molded integrally with the deck. (Those instructions to chop off part of the model were among the first hints that started me thinking there was something odd about the kit. I was eleven years old when my mother bought it for me and, as is probably obvious, I'm still more than slightly pd off about the experience.)
I think the "Beagle" may have had an additional part to make a raised poop deck. (I say that because the Mamoli wood version - which quite obviously is an enlarged copy of the Revell one - has a poop deck. But I don't remember for sure.) I do know the Revell "Beagle" had boat davits, and a couple of new boats in addition to the one borrowed from the Bounty.
The designers somehow missed the indisputable fact that the Bounty's hull was copper-sheathed. (So was the Beagle's, for that matter.) That's really a shame. They did a remarkably good job on the sheathing of their first Constitution kit, which was originally released in the same year (1956).
The "Beagle" kit retains some of the deck furniture and other fittings of the Bounty - and adds some strange-looking, waist-high objects that look sort of like undersized deckhouses. These, like many other features of the kit, have nothing to do with reality.
The one characteristic of the real Beagle that Revell got right was the basic rig. Most of the spars in the "Beagle" kit do duplicate those of the Bounty kit, but the "Beagle" does include a new mizzen mast to give the model a bark rig. (Maybe the ship-rig spars of the Bounty are in the "Beagle" box too; I don't remember.)
Those are the differences and similarities between the kits that my senile brain remembers. Maybe somebody who actually has them in hand can elaborate.
I agree with woodburner: either kit will provide a generic, late-eighteenth-century merchant ship hull. The knee of the head is badly misshapen for the Bounty, but if one were using the parts as a basis for a generic vessel that might actually be an advantage.
The original Bounty kit represented the state of the art in 1956, and still holds up reasonably well against the admittedly meager competition. In many respects it's better than the Airfix version, which is more than twenty years younger. The "Beagle" kit is one of the more disreputable marketing scams in an industry that's been responsible for far too many of them over the years.