The thing that makes Morse and Transatlantic superior is not Portnoy, but Morse in the former and Morse and Roine Stolt in the latter, many other drummers would do just as well playing their compositions...
While I personally consider Morse the single greatest songwriter in the prog world and beyond by leaps and bounds, I do not think Portnoy is just "along for the ride" with respect to his work on Morse's solo material and Transatlantic. Particularly in Transatlantic I don't think it would be just as good without him, both from a purely drum-part perspective and from a writing perspective.
Let's face it, most drummers are not major contributors to the writing process, but if you watch the Whirlwind making-of documentary, Mike has a lot of good input in structuring the music and figuring out what ideas should stay and which should go. I also think his drumming, with Transatlantic in particular, is pretty much exactly what the doctor ordered. He doesn't get completely self-indulgent like he does with LTE or DT, and the production on the drums makes it so they don't overwhelm everything as they do in the aforementioned groups.
I thought Portnoy showed an amazing maturity in his drum work on The Whirlwind. From Dancing with Eternal Glory on, a drummer could have literally ruined the album by getting too showy or tromping all over the space of the other instruments, and instead Mike helped make that one of the most glorious endings to an album I have ever heard.
I think Stolt's work with Transatlantic is brilliant--I love when the guitar is used more as a support instrument to the keyboards than the other way around (which is something that was often true of DT on images and words and completely vanished by the time Moore left the band). Stolt also adds that cool atmospheric, nearly hippie-esque vibe that is essential to the Transatlantic sound. That said, Stolt is absurdly boring outside of TA. The Flower Kings always teeter on the verge of being interesting but somehow never take the plunge out of ultimately boring and vanilla.
So either it's a testament to Morse somehow getting the best out of everyone, or it's just that those guys in TA happen to have some perfect synergy. In that respect, I wouldn't tinker with it under any circumstances; what Portnoy brings to the table is working. This is a band that had a fantastic debut, wrote a follow up that was literally twice as good, and then 10 years later wrote a follow up that was twice as good as THAT; that just doesn't happen.