One thing I noticed was there wasn't an easy way (at least that I know of) to input from different layers and output them to their separate layers without the rules interfering with each other. This is still possible if you separate the input layer indices and then on the input layer you have to place dummy tiles on the empty tile regions you're not looking for on that input or it causes all kinds of chaos. When you do this for multiple layers, this can become a little unwieldy.
If you could do Region[index], and any region that has a number could be linked to the input number, then you could have separate region rules for separate inputs in one single file rather than have multiple automap files.
Sorry if there is an easier way to do this that I haven't figured out.