Ok, after a number of emails back and forth with the folks at Advanced Circuits, I learned that the "industry standard" for solder masks is to print them with positive polarity (i.e. dark where you want solder to go) - you're specifying the reliefs, not the mask around them. Apparently, some shops will accept either and just fix them as needed.
Changing pcb's polarity is a one-character change. Making it a user option is a non-trivial change. So, my question is: has anyone submitted gerbers with positive polarity mask layers, and had it rejected because of that? If the only rejects were for negative polarity, I'll just change the code and be done with it, else I'll need to add a user option in the print popup.
