It wasn't out of place. It would have been awesome in that part of the song if it was actually done correctly. But he unfortunately couldn't keep proper time on it.
It's true the performance was a bit sloppy, but, to me, that's not what ruined that part, but rather the fact that it was placed on a section they forced to be long just for the sake of being long. The last couple minutes of ANTR are spent repeating the same section/riff over and over, just adding or changing small things, it sounds repetitive and just very long, so when the blast beat comes, it doesn't have the impact or momentum it should've had. If you listen to that part, the blast beat doesn't blend at all with what JP is playing, it all sounds empty and just wrong.
The Three Days blast beat works so well because it appears on the climax of the song and was used to enhance the dark tone of that particular section and the narrative of the story.
About the OP, I think MP was the one trying to incorporate more modern elements to their albums, which can be good in many cases, but sometimes it was just too much (ROOOOOOOOAAAAAAAAAAAARRRRGGHHHHHHHHHHHHHHHH). Also, about the Muse influences on OV came mostly from MP, since he's the one who ranks Absolution as one of his all time favorite albums, not JP.
The thing with JP is that he isn't very interested in listening to new bands/new music as Portnoy is. I remember a few recent interviews where JP was asked about new, young bands he was into and he didn't answer any. Like someone said earlier, he's much more into their old influences such as Metallica, IM, Rush, etc.
To me, it seems that Jordan is the only DT member that really goes out there looking for cool new bands and albums. He's the one that had videos in 2013 playing parts of The Mountain by Haken, for example.