Auto-backup backs up the wallet.dat the currently running wallet uses/sees to a folder "backups" which is created in the same folder as your wallet.dat.
If you use different *.dat files in the same folder things may indeed get a bit confusing, but this (advanced) scenario is not what the auto-backup was made for.
It was made for the beginners/non-technical users (which will be the majority if Dash adoption grows as much as we all hope) who most probably don't even know that there is a file with the name wallet.dat and even less know where it is located.
User who already know how to use different *.dat files in the same folder should know how to make proper backups.
BTW, that's the same reason why I implemented the "Open Configuration File" menu. We Dashtalk user know where the configuration file is located, but if you ever had the fun to explain an OSX user where it is located and how to change it you'll understand.
Edit: if it's really needed I could change the upper limit to 50 or more files, no biggie.