Jake, I have found that saw to be the best way to cut glass battens also. I agree that if you had a large deck to cut that a reciprocating saw would be best. Even a small circular saw would be way better than that large, gnarly drill attachment...
I had to avoid the inside fiberglass skin so needed a cut with a somewhat precise depth. I usually use a side angle grinder (large hole) or dremel (small hole) for those kind of cuts. A sanding flap disc in the side angle grinder makes a terrible mess but accomplishes the cut through and tapers the fiberglass skin you will be leaving making it ready for the final glass repair. I use that method if I can be outside on a nice day and use a big fan to blow all the debris toward my neighbors pool. (I'm just kidding about the last part).
