Yes, you can put holes in the diapers. Yes, it will make a mess. I,ve done it both dry and wet. Both are just as messy when it comes to the fluff and pulp/sap from the diaper.
I've seen one method where you prep both diapers prior to wearing them by putting a hole in appropriate spot and use tape (i used cloth backed tape) to seal the sides of the holes back up.
I think the pushing the diaper to the side method only works with some diapers. Cushies seemed to work ok while abena m4 or dry care 24/7 were a bit too difficult to push to the side and proved uncomfortable.
my $0.02