RDiaz, you're not alone. I'm inclined to agree, in fact. The entry ports she has now are beautiful, but it looks to me like the weight of the evidence is against their having been there in 1805.
I know there's been a lot of argument in various quarters about them. A lot of people seem to believe in them rather emotionally. But I've looked at quite a few paintings and photos of the ship prior to her restoration (in the early twentieth century), and I have yet to find a contemporary picture that shows the entry ports.
The big model in the National Maritime Museum, apparently built after her refit shortly before Trafalgar, doesn't have them. (It does have several other notable features I haven't seen elsewhere, though.) The big painting by J.M.W. Turner doesn't have them. The Clarkson-Stanfield panorama of Trafalgar doesn't seem to have them (though there's a brushstroke that just might be an entry port, but looks more like a wisp of smoke). Not one of the old paintings reproduced in Basil Greenhill's and John McKay's book shows them. The McKay drawings show them, but Dr. Greenhill's text doesn't mention them.
The one primary source I know of that shows the entry ports is the other contemporary model of the ship in the National Maritime Museum - the model that apparently shows her in her "as-built" condition. That's a rather dubious source. It's an established fact that not all actual ships matched their "Board Room Models" (which often were built before the ships were), and we know she underwent lots of modifications between 1765 and 1805.
I lean in the direction of believing that the ornamented entry ports were added in the 1920s. But I have no proof of that whatsoever.
An interesting point: the people responsible for the upkeep of the ship herself have been remarkably silent on this matter. I know they hired a carver who (superbly) made new canopies over the entry ports for her pre-2005 restoration. And several publications issued by those folks show the entry ports.
Dr. R.C. Anderson, who supervised the restoration in the 1920s, admitted flat out that the low forecastle bulwarks were "a mistake for which I must bear my share of the blame." He said that research had established that the bulwarks were raised during the refit shortly before Trafalgar, but the researchers revealed their findings just after Dr. Anderson and his team had finished building the low, knee-high ones. They hesitated (understandably) to scrap work they'd just finished, and "the result, while wrong historically, is certainly pleasing to the eye."
I wonder if those entry ports resulted from some similar circumstances.
That Calder-Jotika kit is a remarkable one. (Big caveat: I've never seen it outside the box.) The original release had the low forecastle bulwarks. But everybody who bought it was invited to subscribe to an information service, in which Calder/Jotika sent out pieces of new information about the ship as it was discovered. (Now that's what I call a real scale model company!) The kit as it's being marketed now apparently has the raised bulwarks. (Both new and old versions have the entry ports. That subject seems to be something that manufacturers and the people responsible for the ship are careful to avoid.)
Lots of people know a great deal more about H.M.S. Victory than I do, and if one of them happens to read this post and offers some evidence I haven't heard about I'll be delighted to read it. (How about it, Forum? Does anybody out there know of a piece of actual evidence that those entry ports were there in 1805?)
As for building a model of her...well, I think I'll leave that to somebody else. Even if I could afford that Calder kit, I'm not at all sure I could finish it (to an acceptable standard) in this lifetime. The grand old magazine Model Shipwright sent me one of the Heller kits for review when it was initially issued, in the late seventies; I kept it for several years, but when I moved from Virginia to North Carolina I gave it away. I built lots of models of that ship when I was a kid, and I'm really more interested in less popular (or, to be less courteous, less hackneyed) subjects these days. But anybody who tackles either of those kits has my very best wishes. Either of them has the potential to be turned into a magnificent model.