Well, the simplest explanation is that he's sitting in custody because he doesn't want to be in Hogwarts while Dumbledore scans it for Tom Riddle's soul with the Map, etc. If he doesn't have a particular plot to carry out during the trial, it's easiest to stay in custody then too, until the Aurors choose to release him after the whole matter is considered closed.

If he wanted, he could almost certainly leave, I agree. But why? If this whole thing is his plot, it's going on well enough without him, and on the other hand he possibly can't be officially present at the trial (unless invited by Dumbledore) to rescue it if something goes wrong. OTOH, if it's not his plot, it would still seem to align with his interests - he has more to gain by offering Harry to help rescue Hermione, once Harry has declared the government etc. his enemies, than he does by offering Harry to help sway the trial.