I've been wondering about those entry ports for many years. I raised the question when the Heller kit (without entry ports) was originally released, back in 1978 or thereabouts, and I reviewed it for Model Shipwright magazine. (I mentioned in that review both the Turner painting and the model in the National Maritime Museum - which differs from the real ship's current configuration in quite a few interesting respects.) I've brought up the question quite a few times since, in print and on the web. So have quite a few other people.
One interesting aspect of the issue: I've never seen it addressed by any of the scholars who are associated with the ship herself. Quite a bit of high-powered research was undertaken during the restoration project leading up to the 2005 bicentennial. The researchers concluded, among other things, that Nelson actually died at a different spot than the one long celebrated by the "Here Nelson Died" marker; that she had a couple of long guns, in addition to the carronades, on her forecastle in 1805; and that the forecastle bulwarks probably were raised to shoulder-level prior to 1805. (That one, as a matter of fact, was pretty well known in some circles already. Dr. R.C. Anderson, in a book review in The Mariner's Mirror, called the lowering of the forecastle bulwarks "a mistake for which I must take my share of the blame." It seems that, back in an earlier, major restoration project in the 1920s, they got reconstructed, and lowered, just before R.W. Bugler's book about the ship's history was published. Bugler figured out that the bulwarks had been raised before 1805, but Dr. Anderson, who was one of the administrators of the project, decided not to scrap the work that had just been completed. Money always plays a role in ship restoration projects.)
My own opinion, for what little it's worth, is that the Victory was built with entry ports (probably considerably more elaborate ones than those she has now), but that they were removed during one of her pre-1805 refits. (Probably well before 1805 - and it's certainly possible that she never had them during her active career. H.M.S. Victory: Construction, Career and Restoration, by Allan McGowen and John McKay, contains good color reproductions of quite a few contemporary paintings of her at various dates. Not one of them shows the entry ports.) Just when they were installed (or re-installed) I have no idea; my guess would be during the 1920s. (The Bugler and Longridge books, and the plans by George Campbell and Basil Lavis, all show them. Photos of her sitting at Portsmouth prior to the '20s restoration project don't.)
And I think it's fairly widely accepted now that the forecastle bulwarks were raised before 1805. It's interesting that the excellent 1/72-scale kit by Calder/Jotika was originally issued with plans and parts representing them in their knee-high configuration, but it's since been updated with shoulder-high forecastle bulwarks. (Caveat: I base that observation on the photos on the company website. The kit is far beyond my hobby budget.) I know of only one other Victory kit that shows the raised forecastle bulwarks: the tiny, but remarkably detailed, cast-metal one from Skytrex.
So yeah, Bill, I think you got it right - but I may well be mistaken.
The McGowen/McKay book contains another feature that's relevant to this discussion: a copy (in black-and-white) of one of the sketches Turner made (apparently quite shortly after she returned to England after Trafalgar) on board her. It's a watercolor sketch showing the break of the poop, from a vantage point on the quarterdeck. It shows one more gunport under the poop than is present today (but is present on the NMM model), and a hefty railing along the forward edge of the poop itself - with a swivel gun mounted on it. As I understand it, Turner made several such sketches that day. I wonder where the others are.
When I was younger (a lot younger) I built so many models of the Victory (all of them, I'm sure, pretty awful) that I got thoroughly sick of her as a modeling subject; I'm not seriously thinking about doing another one. If I were, I'd probably start with the Heller kit. Even bearing in mind the various things that need to be changed in order to make it look like she did in 1805 (and the necessity of throwing out all the blocks and deadeyes, the hammock cranes, the poop skylight, the belaying pins, and probably quite a few other pieces that I've forgotten), it is, in my opinion, the best representation of the ship in kit form - with the possible exception of the huge Calder/Jotika one. (It's worth noting that the latter kit - if the photos on the website are to be believed - makes no attempt to represent the "anchor stock" planking of the wales, which Heller got just right. And the guns on all the lower decks of the Calder/Jotika kit are "dummies," with no carriages.) The Heller kit certainly has the potential to be turned into a spectacular scale model, and anybody who undertakes it has my best wishes.