@socbutter First of all I am learning as well as a disclosure as I am not an expert.
For Gain Matching since it is not easy to move subs around and putting them exactly at the same position and same angle is not an easy task, I read or saw somewhere the following is acceptable.
1. In REW using the Tone Generator send the AC Main frequency i.e. 60Hz in USA and 50Hz at other places. You should know what is your AC Mains frequency in your country.
2. Now put a microphone in front of the subwoofer driver 6 inches from the center of the cone. This method works best if your subs have 1 subwoofer driver or your are not stacking subwoofers. Also having a sealed subwoofer gives better results with this method. All these pre-conditions of this method apply to me as I have a single sealed 18 inch subwoofer driver.
3. Make sure your mic is 0 degrees (so facing the subwoofer driver) and not facing up like it is done for taking subwoofer measurements at listening positions.
4. Load the 0 deg calibration file in REW for measurements.
5. Using an SPL meter, put it on top of this microphone and set the appropriate settings like (C weight age, SLOW averaging and appropriate band so the SPL meter does not show over or under warnings). If you do not have an SPL meter then REW will give you an SPL meter if you also open REW's SPL meter in addition to the tone generator using the UMIK-1 calibration file information from miniDSP. If you got your mic professionally calibrated then you can copy that 1st line from miniDSP file to your calibrated file to get a rough idea of SPL.
6. Now you send your 60Hz or 50Hz tone depending on your AC Mains frequency at any level (-12 dbFS or - 30 db FS) and take a reading on your SPL from the 1st subwoofer.
7. Move the mic and your SPL meter (if applicable) to the other subwoofer. Send the same single and take reading.
8. If both subwoofers should have the same SPL then you are gain matched. If not, you can adjust the one that you like as they will be pretty close if the subs of same kind.
FYI, as an additional TIP, I connect the USB output from my laptop directly to the USB input on my minDSP and switch the miniDSP input to USB instead of the typical ANALOG. This bypasses all the AVR issues you have mentioned above because the goal is to first get an aligned virtual sub created in your room which is then used as the single sub that the AVR should see and use for its calibration.
Hope this help. Good luck!