Yeah, assault carriers stuffed with units are pretty ridiculous.
Their effective-DPS is sky high since usually your fleet would lose damage as ships get taken out, but with these guys their damage is consistent and good enough to take on decent sized fleetblobs and high level turrets without sustaining basically any material loss. That and the points you've stated, the cloak/alpha strike capability, auto free fast repairs, and blazing fast speed makes me personally feel that they're borderline OP for what they cost (in K and in metal).
I actually have a personal house rule to never shoot stuff with assault transports due to this reason. Doomdropping your entire fleet on top on an AI emplacement may not be as efficient as blowing them up with the assault transports themselves, but sure is a lot more fun.
Dunno, perhaps the current assault transport can stand to be moved to Mark III, and a extra tier be added between the current assault transport and vanilla transport, which won't have the ability to fire but keeps the other toys (cloaking, speed, repair in friendly territory, etc).