Your indie can certainly be correct in that the battery might hold a charge just fine and your alternator is functioning properly as well. What might be happening is something intermittent is severely drawing current and wiping out your battery without you ever knowing it. (Did your battery charge light ever light up? My guess is that it didn't.) For some people it's a malfunctioning lock mechanism that cycles all night long. For others it's another system that keeps turning itself on, going back to sleep, and doing that continuously. It's a problem that really sucks (no pun intended). Your best bet is to give it to a good shop to spend a few days looking for the drain, but if I were a betting man I'd say it has something to do with your alarm system given the order of events that you describe. Some part of it I would bet is draining your battery big time.

Until you do that I would not lock the car using the remote any longer and use the key in the door (make sure all the other doors are locked though) so as not to engage the alarm. I'd also keep a good set of jumper cables with you at all times or a quality jump starter that is easily accessible. Don't forget that if it's completely flat you won't open the trunk. If you need to get your cables or jump starter out of the trunk then it's going to have to happen by folding down one of the back seats.

Also, when it happens again drive it immediately to the shop. I think it's one of the instances when connecting to a battery charger doesn't really help you at all since it will only mask the problem and slightly delay the inevitable.