Okay, for the first time you are acknowledging that you have to power the module from 3.3V. But there is more you need to do, which I already outlined above.
The SCL/SDA lines coming from the module are connected to 5V on the module via pull up resistors. If that is not connected to anything, what you get is a series combination of R2,R4 = 20k ohms right between SCL and SDA. I don't know about you, but that makes me feel uncomfortable. It means that if one is pulled low, the other can also be pulled partly low. Also possibly backfeed current through the regulator. Not good.
VIN and Vdd are adjacent on the module connector so it's a simple wire jumper to connect them. Providing 3.3V to both, you would have to solve however you like. I would cut the 5V trace coming from the Portenta, and jumper between that and the Portenta's 3.3V pin which is two pins down the row. That way you can still retain the bypass caps you have in there.