I would avoid that actually. The way you describe is probably compacting the soil. Indoors, cultivating your pots isn't necessary, and I personally would just poke holes with a chopstick and besides that, let them be.

I'm still wracking my [small] brain to think of other reasons. I'm sure this is a combination of multiple factors here... hmmmmm....

Where the heck is rhizome when ya need him? This is one of those stumpers fo'sho!