To be honest, I also don't mind the band taking more time to work on TA5. I think one of Mike Portnoys major flaws of the past decade (and thats criticizing him on a very high level, so please don't get me wrong) is this weird concept of getting together, writing, recording, tracking and mastering an album IN THE STUDIO in a couple days and then just moving on to the next project. Thats how Sons Of Apollo do it (which you can totally hear in their first two albums) and it's also what he likes to do with other projects.
Regarding the bolded part, no, that's NOT how SoA do it. I don't know the full story behind the debut album, but I know that's not how MMXX happened. While the basic songs may have been written out within a short period of time, and MP laid down his drum tracks, that doesn't mean that all the other guys banged everything out at the same rapid pace. In fact, I had heard that the other guys worked on their respective parts, building on to what was written during the initial writing session. Also, the fact that JSS and Billy were not involved in the initial writing session certainly gives credence to this (which was also the case with SoA's debut) - each needed time to work on their parts - especially JSS in writing lyrics and coming up with vocal melodies. So unlike LTE where everything was banged out within a matter of a week or two as you posted, this was not the case with MMXX and probably wasn't with the debut, either. And I'm pretty sure this is similar to how Flying Colors and TA both work.
Having recently re-watched a lot of the Making Of documentaries for Transatlantic and Neal Morse albums in the last few weeks, I can say that, while the writing sessions may take a week or two, the songs written are usually based on demos by the band members, some of which may be YEARS old by the time they get into the studio. Transatlantic's studio time isn't JUST writing, but also arranging and crafting songs from various demos by Roine, Pete and Neal. Even when they are done arranging the music, and Mike tracks his drums (sometimes during or right after the writing/arranging sessions, though in the case of TA 5, Mike tracked his drums weeks/months after the initial sessions), the others take their time to refine and record their parts and overdubs. The lyrics and vocals may not even happen until months after the initial sessions, and the albums don't even get MIXED (let alone mastered) until several months, or over half a year, after their initial sessions.
The idea that they do all of their "writing, recording, tracking and mastering an album IN THE STUDIO in a couple days" is really hyperbolic and really downplays how well Mike works with his fellow band mates in his various projects. If all of the music sucked, then yeah, it could be a problem, but bands like Transatlantic, Flying Colors, and even Sons Of Apollo and The Winery Dogs, all have wide fanbases and many of them love the music they all put out, so if it ain't broken, why fix it? Mike's working formula works, so until he gets a HUGE bomb on his hands, I doubt he'll change his methods. But as Scotty said, it's not just Mike that makes these albums possible, and his band mates do continue to work on the music months after their initial sessions in the studio.
-Marc.