Was on site today - the box itself also doesn't seem to be straight - the opening where the push plate goes on one side is about a centimeter further out than on the other side. Seems like the box is not parallel to the wall :(
Did you ever put a spirit level on top of the box or is the front wall floor-to-ceiling?
And do I understand you correctly that the flush plate will be crooked?
Where the flush plate is, everything is level but it sticks out further from the wall on the left than on the right. According to the plumbing company, this is still okay because the toilets are supposed to have enough play. Well...