You’re right about the MHD version having some differences from the theatrical/video version; however what that last post is referring to is the fact that Kraken Releasing’s Blu-ray adds the dialogue track from Toho’s export dub to the music/sound effects from Toho’s 5.1 mix of the Japanese version, as opposed to using the existing mono mix. There are also two different mixes of the music/effects for the Japanese version, the most notable difference being that death cry.
I might eventually revise the audio track on my reconstruction to match the theatrical/video version, but for the time being I’m moving on to other projects, seeing as the current version is already almost completely visually accurate.