I think the "production scare" for DT should have worn off after just a few years.
Ok, I get it - the record label comes and derails Falling Into Infinity (and eventually we found out that not even all the band members thought of it as a derailment). They want to do things their own way and they make one of the best album ever as a result, awesome! So they self produce... and grow bigger... and bigger... until they are well estabilished, respected and continously sell out big venues, or at the very least, fill them.
I wouldn't know how to pinpoint the exact point in time where a producer would be "safe", but I daresay that after DT estabilished themselves as a leading act, no way the FII nightmare would happen again. No way a producer would come in and go "Lol let's hire someone to write a catchy chorus and please make shorter songs". A producer that gets, understands and respects DT would have done wonders with them.
This is not a knock on Petrucci coproducing the albums, not at all. But I just think that if their rationale for skipping a producer like the plague was "Record label screws it up", they've long been in a position to say to the label "Look, just let us do what we want to do", and a producer would help them, not hinder them.