Maybe it makes more sense to leave it as it is, then the custom configuration file gets backed up by the user and should persist over any future upgrades to the extension, the 99 on the custom conf file means it loads last I think.
But I guess if 10-evdev.conf is writable then it's up to the user how they do it, either way will work.
I'll leave it with the dev people to decide what makes most sense, but for my application I think I'll stay with the 99 file as an add-on to the standard install package.