The precise configuration of the Victory at Trafalgar is a complex matter, with no definitive answer. I wouldn't be comfortable asserting simply that the two smaller kits represent her at a later date than the big Heller one does.
Over the past thirty years I've brought up the question of the entry ports several times in various places. She almost certainly had them (in a considerably more elaborate form than the current versions) when she was built. Several paintings made shortly before and after Trafalgar don't show them - most notably the enormous oil by J.M.W. Turner in the National Maritime Museum ( http://www.nmm.ac.uk/collections/nelson/viewObject.cfm?ID=BHC0565 ). They're also absent from a contemporary model in the same museum ( http://www.nmm.ac.uk/collections/nelson/viewObject.cfm?ID=SLR0513 ), that model having been (apparently) built after the ship's 1803 refit. And they don't appear in any photographs of her prior to her restoration of the 1920s.
None of that, however, is absolutely definitive. Turner was a great artist, but his understanding of technical nautical details seems to have been pretty hazy at times. It's known that he went on board the Victory shortly after the battle and made sketches (some of which have survived), but he didn't finish the big painting till 1822. It's entirely possible, I suppose, that he paid another visit to her during the intervening 17 years and, without knowing that he was doing it, mixed up some details that had been changed. Or he might have simply overlooked the entry ports completely, and made an outright mistake; artistic types have been known to do that sort of thing.
The ship got a great deal of attention, from people who know far more about her than I do, during her most recent restoration (in the years leading up to the bicentennial of the battle). They left the entry ports intact. The entry ports appear in every reputable set of plans for the ship I've ever encountered - including those by Basil Lavis, George Campbell, and John McKay. I have, in fact, never read anything about the presence or absence, or addition or removal, of the entry ports in any of the published sources about her. I have to say, as a matter of fact, that prior to reading Warshipguy's post I was under the impression that the Heller designers, J.M.W. Turner, and I were the only people on the planet who thought the entry ports might not have been there. (I've noted that several modelers taking part in other web forums have asserted pretty emphatically that they think the entry ports were there in 1805 - but none of those folks has explained why he thinks so.) I'd certainly be receptive to any further evidence. I really wish Mr. Goodwin, or somebody else connected with the most recent research project, would address this question and tell us definitively what the evidence on both sides of it is.
In any case, the entry ports are only one of the problems confronting the modeler trying to reconstruct the Victory's 1805 appearance. It's now pretty widely accepted, I think, that in 1805 she had shoulder-high bulwarks around her forecastle deck. One of Turner's sketches shows a huge, bulky railing, with a good-sized swivel gun mounted on it, at the break of the poop. The contemporary model in the NMM shows similarly clumsy, open rails all around the forecastle and poop, somewhat different decorations on the transom, and a conspicuously different bow structure (with an additional knee - which I haven't seen depicted anywhere else). And the number of gunports on the model also doesn't match the ship's current configuration.
I don't think anybody will ever figure out exactly what she looked like in 1805. For the vast majority of onlookers, the Heller, Airfix, and Revell kits probably come close enough. (I continue to think there's something wrong with the shape of the smaller Airfix kit's bow - but that's another story.) I certainly agree that the big Heller kit (sometimes sold in an Airfix box) is one of the finest plastic sailing ship kits ever. And I most emphatically agree that it's not a good project for newcomers to this part of the hobby. But having said that dozens, if not hundreds, of times during the thirty years it's been on the market, and having been ignored every time, I won't bother pursuing that point.