Thanks @iagorubio and @dartd for your replies. I agree it can be an electrical issue between the Irisv2 board and the transceiver, but I have my doubts. I connected the other available CAN port in the SoM to the transceiver by using very small DuPont cables (far from ideal, I know) and it works. The very same thing against the first and official CAN port and it does not works.
In both cases the transceiver is connected to another transceiver connected to an RPi, and I can send and receive packets without issues.
The fact that I am also having issues setting other pins as GPIO-keys makes me think I might be missing something very important here or somehow I’ve got to screw the module :-/ (although I do not think so, but well, let’s not discard it).