Sorry, I forgot to say that I found a solution, so there it is:
The HX711 is a blocking-reader sensor, which means that when it is doing something, the ESP32 only does the reading and "stop" everything else. Moreover, having multiple IO blocks in a Simulink model seems to always create issues. Simulink tries to access and launch a C code on the ESP by opening Serial communication (if XCP Serial is chosen of course), and when there is multiple blocks the task gets confusing and many times, the error : "XCP serial port error: serial port send error" will appear.
To avoid this from happening, the sample time can be set the same for the two IO blocks. But, and yes it's that simple, the HX711 one, which is supposed to be executed first, has to be manually set to priority "First". In that way, Simulink will open the connection to the sensor first, then open the CAN bus.
However, and I am currently on this issue, when there is a third IO Custom Block, for another sensor, this is not working anymore. The second sensor is using Serial(2) so it should be a different way of communication to the ESP. But I still get the XCP error even after changing the priorities. I think I will just create a new model and run it on a third ESP32.