I've struggled with this concept a lot. If you have something in the car 24/7 stashed away, it can't really be a beater. You need something that's reliable and a good 'fighting pistol', and not finicky about dirt or lubrication since its going to see a lot of one and not a lot of the other. If you need it, you want something right. If someone steals it, you want one of the aforementioned high points.
So do you stash one of your oddball/unloved pistols there so if it gets damaged/stolen/rusted/whatever you're not out anything, and go with the "any gun is better than no gun" if you need it, or do you put a copy of your favorite/EDC-ish pistol in there so when you need it it's what you're proficient with?
One answer would be to EDC a high point!
The theft angle bothers me a lot. Yes you can lock them up, and bolt the box down, etc, etc. But bad guys get their guns by stealing them from good guys. I don't want to be the good guy that arms a criminal.