Hi Simon,
I think we need to clarify something here. Whilst the film on Blu-Ray is indeed very, very good, there is a version of "WITCHFINDER GENERAL" known as "THE CONQUEROR WORM" that contained alternate, more raunchy/violent footage, that was not in the regular "WITCHFINDER GENERAL" release.
This alternate version, is also known as the Export Version. On the old Metrodome DVD release, the two scenese were re-edited back into the standard theatrical version, and the jump between the high quality theatrical print, and the lesser-quality "Export" footage was noticeable....
Whilst what you say is broadly true, I believe you're confusing several different issues here. My understanding - based largely on Benjamin Halligan's book on Michael Reeves - is as follows:
There were basically three different original theatrical versions:
- The UK print with BBFC cuts made to about six scenes, all for violence (the priest's torture, the duckings, the burning, Sara's torture, the torture of a woman in the neighbouring cell, the killing of Hopkins)
- The US print with none of the above cuts, re-titled
The Conqueror Worm (to fit in with AIP's Poe/Price cycle) and Poe voice-overs to explain the new title
- The continental (or "German") prints, not re-titled and with none of the cuts, but
additional nudity in the tavern scenes. These were re-shot by producer Tony Tenser and Reeves was not even present when they were done, so they have nothing to do with the film as he conceived it.
The DVD releases I'm aware of these:
- The UK Metrodome DVD that presents two totally separate versions:
1) The UK version, as it was intended by Reeves, with all the cut violence restored, but in poor VHS quality.
2) The continental version - exactly the same length and indeed identical, except for the additional nudity in the tavern. As the latter scene is in excellent quality, but the restored violence is from tape, it's obvious they were from different sources and Metrodome were unable to find a complete film print of the continental version. I suppose the tavern scene had been stored in 35mm as a sort of outtake, and the violent scenes came from an old TV broadcast or VHS release outside the UK, but that's just my speculation.
- The US MGM DVD which presents the UK version (with the original title) as it should have been before the BBFC cuts, with no discernible drops in quality. My recollection is that they simply transferred a US negative or print (substituting the original UK titles) as the film had never been cut there, or perhaps they even had a complete UK print. (The US DVD was long delayed due to copyright wrangles over the music, which had caused previous US releases on laserdisc and tape to use a new score!)
- The UK Odeon DVD & Blu-ray which I haven't seen but I gather present the film in the same version as on the MGM DVD, with the nude continental version of the tavern scene (never part of Reeves' conception) as an extra.
Simon may be able to clarify further.
So, yes, both releases are "uncut", but they still include footage from other prints, that are not up to the same technical standards, as they were taken from VHS sources. No new sources have been found, as of yet, that are superior to these, and the distributor's have said that it is unlikely that better quality footage will ever surface of these two "scenes". 
