We do this all the time in the plant I'm in. Many advantages: 1)Makes for a snap to add new pipes in limited spaces. 2) Can run new pipe and wire into gutter w/o shutting down the panel - only shut down for final pull and connect. 3) You run outta KOs on the top fast and the pipe job gets ugly when you have to snake 15 - 20 runs into the side KOs - even pull ells don't help sometimes. On jobs where this wasn't done, the panel top might have been made of chicken wire for all the strength it had after it was punched.
We deduct the volume of the pass thrus from the volume of the box for fill calcs, but that is the engineer's or AHJ's call to make initially.