We ended up deciding that updating the BG95 firmware was an acceptable solution. By updating from BG95M3LAR02A03_01.012.01.012 to BG95M3LAR02A03_01.015.01.015 we had a second at port in "usbnet" : "modem" config mode, which solved our initial issue (we needed two AT ports but had only one available, as explained before). I think this update also allow the modem to be configured in "usbnet" : "rmnet" mode, which should allow you to communicate with your modem through QMI.
Hope this will help, in the end the only solution we found was to update, sorry 