Mechjeb can do many tricks, though when you ask it to do something that has to happen in the future, mechjeb will just accelerate to the burn moment and then starts orienting the spaceship.
Would it be possible that if mechjeb knows about a certain manouver "in the future" that it will first align the craft before going into timewarp, so that when the moment arrives it can burn instantly instead of having to wrestle a big ship into orientation while the burn moment has passed.