You should be able to still use the two channel trim, just don't exceed -15db total between it and the normal channel trim. The solution is to turn you sub amp gain down if you are getting close to the -15 limit.

Here's how I found it.
I had my 2 channel offset at -3 db.
Sub calibration tone jumps when going from -12 to -13. -16db total.

Change two channel offset -2db.
Sub calibration tone jumps when going from -13 to -14. -16db total.

Change two channel offset -1db.
Sub calibration tone jumps when going from -14 to -15. -16db total.

No two channel offset works. -15db total.

The levels must have changed somewhat because I hadn't touched my sub amp gain since calibrating with the old FW. I also have a very efficient room and powerful sub. I currently have my sub amp gain dialed down to about 1/4 and actually need to turn it down a little more to get the trim number to around 0 instead of negative.