Lastly, I got an email reply from David Jirkovsky of SCT. He confirmed the 3.91 ratio is supported but not as a directly selectable parameter. David explained the adjustment comes through as a ratio of the stock factor. Below is the direct cut/paste of him explaining the setting:
Yes there will be support for that, but it wont be listed as 3.91, you will have to change it by percentage of increase. So whatever stock is, you would divide 3.91/(stock) and you will get a number 1.xx. That xx is your percentage increase. So if they are 3:45 stock, it would be 3.91/3.45 and that is 1.133333 so your percent increase is 13% and you would set the tuner to 113.
I followed up by asking if that is a USER selectable setting and not a custom tuner setting, and he confirmed it was USER.
So SCT WILL DO our 3.91's off-the-shelf, and without a custom tune at an added expense.