You can upgrade the firmware version to 2.9.1200 without any worries, it is even recommended to upgrade the firmware to the latest.
The latest firmware version is not build-in in the driver because MNPH29C-XTR is an EOL (end of life) card and also reached to its EOS (end of support) period and is not maintained anymore by MLNX_OFED driver but there should not be any problem to upgrade the firmware separately from the driver.
Thanks Viki for confirming that for me.
I initially though it was checking online for a newer version, and was failing due to the A2-A4 and A2-A5 Part Number discrepancy, but if it only checks what's included with the driver then that makes sense.
I'll go ahead and flash the newer firmware and see if that does anything to fix my boot issue.