So, Vae Victis, you can sleep quietly: this version is the only "legitimate" one, any movie historian can confirm that.
If you consider the case of "The Flesh and the Fiends" for instance, another British movie, some scenes were filmed twice, one with clothed girls, the other with naked breasts. However, in this case, both versions were filmed by the same director, John Gilling, so both versions can be considered as "legitimate".
In the case of "Matthew Hopkins - The Witchfinder General", these short "nude" sequences were filmed AGAINST the director's willingness, by someone who was the representant of the American coproducer.
Eventually, they could have been included in the DVD as a bonus; but their inclusion in the movie itself would have been intrusive. And the same goes, of course, for all the other changes made by AIP. They are no more "legitimate" than all the changes made in Hammer films like "The Evil of Frankenstein" in America, when Universal shot additional sequences (with actors even not involved in the original film !) for the television showings of this British film... (happily enough these ridiculous sequences weren't included in the US DVD !!!)
For Spudthedestroyer: No, the DVD is NOT missing any gore, as we have exactly the same version in Europe, and all the violent scenes are intact as I wrote above. The ONLY differences are the things which were ADDED to the original British film in America. And the nude sequences... read above !!!