Thanks @maxgerhardt for your suggestions.
I will try testing these “intermediate steps” (in-between of the two complete boards descriptions that I have), hoping I can narrow down to the problem/conflict/difference(s) between the two boards.
FYI I have followed the tutorial you pointed to create my boards. Maybe I created some conflicts or failed to change
I was not aware of build_board.variant, it seems useful (at least for the case I’m facing) but I doubt I can use it further since my board custom board is actually using not exactly the same CPU, not pinmuxing, … (H743ZI for Nucleo, H743VI for Custom board). I have also some shields overlays. So I’ll probably stick to two differents boards structure in the future.
Something I tried as well is to flash the firmware.elf generated by NucleoH743ZI environment (working fine on Nucleo board) to the custom board. It still crashes at runtime the same way. Indicating there is definitely something bad at HW/DTS level, eventually at USB/CDC level. I’ll check the errata for the two MCU as well maybe to spot something.