I don't see anything wrong with Mike saying this. I realize that he sometimes says things he probably shouldn't say, and this is a case where this casual comment will blow back on him, but the interviewer asked him specifically about Rush covers, and this seemed to have been a fairly long term project relating to Rush covers. I think he's completely justified in being bummed that he never got to release that bootleg and even in expressing that emotion, even if it's not the best PR decision. And he's clearly not blaming the band for that, he's just saying that it's a shame that because of the way things happened he never got to release those to the fans.
Of course, the dream is that some kind of deal is reached where Mike allows material from his archives to be released in the future by Ytse Jam Records. I don't know what that could involve, possibly royalty payment and a producer credit for MP. But I suspect that will not ever happen because a) the band does not seem to have a whole lot of interest in Ytse Jam and b) Mike Portnoy has mean mean pride.
Still, my point is, I don't see the problem with what Mike said there. The topic of conversation was Rush covers, so he brought up a Rush cover project that he'd obviously been working on for quite a while and expressed regret that the situation with him having left the band means that that project will never be released. All of which is totally justifiable and none of which constitutes a shot at the band.