Thank you for your reply, especially during the long holiday weekend in the USA.
I ended up solving the issue in a different way. From this post https://forums.xilinx.com/t5/Xilinx-Evaluation-Boards/Enabling-VADJ-on-ZCU104/td-p/861259, I found out that there is a bug in the FSBL. Instead of reading the EEPROM of the FMC card, it interrogates the EEPROM of the ZCU104 board. Since I have the Infineon USB005 dongle to write to the EEPROM on the ZCU104 through I2C, I used it to reprogram the value to 1.8 V and it worked.
Patching the FSBL is probably the more elegant solution, but I am a bit time constrained at the moment. Also, I am more confident messing with HW rather than SW or firmware.
Thanks for the help!
PS: unfortunately, I cannot mark both answers as a solution. So, I will mark this as a solution since it is the one I tested.