So what I've gleaned from this is that now that MP's out of the band and has been for a while, he feels that he can comment on DT's music the way he did as an impartial observer/listener/fan in the same way that any other fan might.
The fact is, given who MP is in relation to the band and his history with them, his opinion of the band's recent output tends to carry more public weight than your average forumer.
Even if he doesn't intend it as a potshot at the band, it's so easily interpreted as that because he was such a big part of DT for so many years, and because he left under rather ugly circumstances. If anybody else said "wow, This Band's song "X" sounds exactly like DT's song "Y" it's not going to be interpreted as a "serious accusation of plagiarism." But when Mike Portnoy does, it is. It's been a while, he probably doesn't harbor hard feelings toward the band, but feels far enough removed from DT that he can publicly say stuff like this and not have it be a huge deal. The rest of the world still very much associates MP with DT, so the end result of all this is that we all still care too much about what Mike Portnoy posts on his forum.
A friend of mine close to members of DT tells me that MP recently sent the whole band an e-mail apologizing for all the mud-slinging and congratulating them on the Grammy nomination.