Is a "pro tune" just an experienced professional using the tuning programs? Or does it involve something more, like using a dyno?

 

It's both it just means someone is tuning the car for the modifications you have, and specific to your vehicle. That can be done in person on a dyno, as a pro-tune. Or you can get working with a remote tuner which is an e-tune but is still a protune, as it is as above, custom to your car and the mods.

E-tuning takes a lot longer as they have you log, send you a tune, log, send you a new tune etc.. A pro-tune can be done in person in one day if it's just a tune, or longer if you are adding parts, depending on the parts you are having them add.

 

This ^^^

 

Pro-tune is as opposed to off-the-shelf (OTS) tune. Many amateur enthusiasts buy a basket of mods (called "stage x package") and get a OTS tune, so to take advantage of how cheap that is. Generally this works out for most naturally aspirated (NA) cars like some K24Z7 / K20C2 Civic or V6 Mustang. However, for a turbocharged Evo X where the engine is complex and sophisticated, pro-tune is the only available choice.