The coconut fiber is fine, and won't be a problem if your snake ingests a little bit of it while eating. No need to pack it down.

Also, I'm not sure if it would be easier to clean if it was packed down. The stuff absorbs pretty fast, so you would have to replace whichever amount get soiled no matter if it was packed or not.

As far as clogging the heat pits... I've never heard of such a thing.