I have a theory that it just kind of happened organically.
I remember checking setlist.fm shortly before Portnoy left, and according to their statistics, the top 7 most played live songs by Dream Theater were all from Images and Words . "Wait for Sleep" was the odd song out (and even that was still in the top 15), and "Pull Me Under" was the in the lead, having been played over 400 times live as of 2010, with three other tracks from the album also over 400 not far behind, and three others over 300. Everything about those songs, including their structures, must seriously have been written into their DNA by that point. If you asked Petrucci for the structure of "Metropolis", he could probably recite it to you off the top of his head, verbatim.
So imagine they are siting down to write A Dramatic Turn of Events, their first album without Mike Portnoy in the band. Those songs are so ingrained in their mind that I would not be surprised at all if they just started writing songs that (quite unintentionally, mind you) mirrored the structures of tracks from I&W and didn't even notice without someone else pointing it out to them.
So how come it never happened before?
Because I have a feeling that Portnoy, who was so famously neurotic about details and a major player in the arrangements of their songs, probably prevented it from happening before. If Petrucci and Rudess had written a song that too closely followed something they had done before, Portnoy probably would have said "we have to change that, because it comes to close to 'X song'", unless he wanted to make it an intentional nugget. ADTOE was the first time they had ever written an album without Portnoy, so he wasn't there to point out to them that what they were writing was so similar to songs they had been playing for nearly 20 years at that point.
So I don't think there was anything sneaky or underhanded or even conscious about the whole thing at all. I just think the band subconsciously wrote songs that fit those I&W structures because they were so deeply ingrained in their minds, and Portnoy wasn't there to stop them this time. That is probably why Petrucci denied the rumors that the band was intentionally ripping off their past, because they didn't do it intentionally; it just kind of happened, and that band probably didn't even notice it until Thaigo started posting about it online. At that point, they would never admit that they had "accidentally" replicated the charts, because, frankly, it would have sounded embarrassing, and no one would believe it anyways.
Incidentally, it will probably never happen again, because if they weren't keeping an eye out for that sort of thing before, you can be damn sure they are keeping an eye out for it now!