Why the first album should have a remix again? I have the Dark Genesis boxset and the remix (or it was a remaster?) on all the first three albums is excellent, in my limited exploration of remixes I'd say that, at least in heavy metal, those are by far the best ones where the difference is clear as night and day, and there's no need for any further tinkering.
About Jon... he's always made it clear that he has an altar where he worships Steve Harris and he's always been brutally honest about having a vision for the band and taking no prisoners in aiming for it. As it has been said, he has no filter like Portnoy, but maybe he's just a meaner than Mike (For all the bad rep Mike got for his online comments, his personality first and foremost as a music lover with tons of knowledge always shines through).
It's all a matter of personality and being your own filter I guess, Bosk said more than once that Petrucci has strong opinions and he's probably a firm leader like anyone else, but he always comes across as a nice and humble guy. Which I'm quite sure he is anyway, but I don't think we will ever see him (or read about it on the internet) blatantly in "I am the boss" mode, because even if he is, he's able to keep it hidden.