I have the same tail bag and I've been using it for commuting, rain or shine. It's been working great. I also got the matching saddlebags for going on long trips. I tested it by doing a grocery run. I can fit almost 2 grocery bags of per compartment. Pretty good.IMHO, the lack of 'safe' bungee hooks in the rear is the one design shortcoming of this bike. Having the plastic tail section stick out where bungee cords are going to rub is the second flaw. I'll be using some clear plastic protector on mine, as you mentioned
Anyway, going back to the comment on lack of rear bungee hooks. I thogh of doing the same as the OP, hooking it underneath the tail. but then it will get all nasty from riding. and then the bungees would retract back into the bag, geting the inside dirty. No good. So I hook the rear bungees to 2 metal connectors behind the license plate. seems to work well for me.
Also, the front bungees do rub against the body work. I thought after sometime, it would rub thru the clear coat and eat thru the paint. So I put a couple of layers of 3M heavy duty packaging tape at around the area. It's clear so you can't even tell. Once it gets worn and dirty, just peel it off and put on another layer. Problem solved.
Below is my post on my saddlebag and tailbag in a different thread.