It appears that although they marketed the 2014 Italian release as a restoration of the trilogy, they only did 4k scans of FOD and GBU (and made them both green/yellow). It looks like from the stills on this page linked below that they used the old scan of FAFDM.
http://distribuzione.ilcinemaritrovato.it/per-qualche-dollaro-in-piu
Currently the only way to get this movie uncut is to buy the German version, the Italian version is still cut by a few seconds during the beating scene. The German version uses some poorer quality materials to fill in the missing material, but at least it's complete.
For some reason I was under the impression the German BD looked better than the US.
I just realized it's not true...at least not on my set-up.
So I just re-watched the US BD and there
is a crude edit between the beating and Indio's following dialogue.
I gotta put the German version on and see if this is where the footage was cut.
I wonder if it was some absurd ruling where 1o seconds of violence was permitted but not a second more?
Also, concerning the thunderclap, with Manco's introduction... both have it mistimed.
However, the US version was much closer than the German release which helped in my decision on what disc to watch.
The German release wasn't even close
I noticed the problem lies with a break in the music during Manco's entrance.
I hope Kino has this fixed but I won't get my hopes up since their releases have been less than stellar lately.