I'll let the more experienced woodworkers offer their opinion, but I have had some boxes that looked like that and once they get filled up with frames and honey, and bees, etc. they just sit down tighter. Also once you place the top on that pushes everything down more.
The supers are always stuck together about the same as I can remember and never a problem in unsticking them with the hive tool.
I think you don't have to worry about it.
Maybe more water can seep into them, not sure. I don't have any problems with irregular hive parts. As long as the bees can't fit through them.