Well, the ones that Adafruit has on the module, are connected to 5V. So not really correct for a 3.3V processor. I don't know about diagnostics. I don't think it would help in this case.
Really, the brutally simple solution is to put a level translator between the module and the Portenta. Then no mods needed.
Are you connecting to the pins called "I2C 3V3" on the Portenta schematic?
Edit - oh I see it now! Jumper the 5V to the 3.3V pin on the magnetometer board. Power both pins from 3.3V. It will work fine on 3.3V that way, and interface properly to a 3.3V processor.