It's true, the MHE BD does have a minor cut during the beating scene. Here is a comment I posted on forafewdollarsmore.net:
"...the MHE blu-ray of FAFDM is also cut in an unusual way. The scenes of Manco and the horse in White Rocks and Indio’s laugh post-prison break are uncut. However, although the missing dialogue post-beating of Manco and Mortimer is there, there is a small cut during the beating scene that I have not observed in any other version (VHS, laserdisc, MGM BD, DVD). During the beating, Manco briefly fights back, gets punched and stumbles back, but there is a cut in the MHE BD at this point and you don’t see [Manco] stumble. It’s a minor cut but just proves that there is not a BD/DVD out there that is totally uncut."