It seems as if WB once planned releasing the Batman vs. Superman Ultimate Edition 3-hour cut in IMAX theaters.
Footage from the Batman vs. Superman Ultimate Edition has hit the net in IMAX (see below); however, I believe the movie in its extended form never was released in IMAX.
WB did release the Batman vs. Superman Ultimate Edition in theaters for one night only in select cities, but I don't think any of the theaters were IMAX.
It's possible WB went with an IMAX version as part of that re-release, but for whatever reason decided against it.
Batman vs. Superman has taken a lot of heat, but I really enjoyed the 3-hour Ultimate cut a lot more. Don't get me wrong, there is still stuff I would change, particularly in regards to Superman, but I've actually watched the Ultimate version a couple of times and still enjoy it.
The Batman vs. Superman IMAX footage features the Knightmare Batman scene with footage included in the Ultimate Edition, so that's how we know an IMAX release of the Ultimate Edition was at least planned.