I would expect gnome-firmware to update the UEFI without erasing user settings. What’s the worst that can happen if it does?
- you’ll need to setup custom settings in UEFI again, there should be very few of those
- it may clear the boot order and not find your Manjaro grub loader as described here
Other than that it should be a regular operation. Just don’t turn off your computer while it updates 
And keep bootable Linux USB drive ready to register the bootloader to boot again.
Your LUKS2 volume is totally independent of the boot, it does not rely on any hardware like TPM (safe assumption?) Say your computer died, you can still pull out the SSD/HDD and use it as before in another PC as long as there are no driver issues.