Thanks for the suggestions. I guess no bag will be perfect, so my best options seem to be to put a good light under the bag and then use some extra lights. I have a blinky on the back of my helmet, but it's a cheap freebie I got so I'll keep an eye out for something better.
And yeah the MK3 is ugly, but beautiful in comparison to how filthy my bike got after my first real ride this winter when I was fenderless.