You're absolutely right.That is planned for a future fix.
Right now they want to make it run properly
You are right again. In the database the channels and your editing on them are stored.I believe this version creates and imports the current list into the database directly.
Opposite to other supported sources tvguide did not provide a simple list of the available channels. That's why there is a one day EPG grabbing for all channels performed on every start of EPG-Buddy. This way we get a recent list of the available channels that we store (and update) in our db. In daily usage (means as soon as you're done configuring your channels) the main program is not running. Only a few helper tools (without GUI) that does the automatic data download for you. The "real" EPG grabbing then is for the configured channels only to save bandwidth and time. The downloaded EPG data only is stored inside the resulting xml files, not in the database...