Why does the Portenta mismatch buses between the high-density connectors and the internal STM32? This really seems like a nasty trap for those not paying attention. It certainly took me a long time to notice. I'm sure this is more obvious in Altium, but I only have the PDF to work with.
Please rearrange your post so the question is in your post, not the thread title. That can become confusing.
The Arduino core creates device names for all MCU resident pins. It is those names that the programmer sees - for example UART4 in the diagram above. It may actually be UART0 in the STM scheme, but it would only be confusing to someone who is referencing the MCU via STM designations. That is not the case with someone using the Arduino IDE.
Edit - thanks for updating your post.
Thank you for your answer. That makes sense. However, I do not plan on using the Arduino IDE, and this does not account for the alternate functions of the pins. It just seems needless to me when they could just as easily use the same naming. I see an argument for compatibility between Portenta models, but I would still argue that if the buses are mismatched the pinouts aren't perfectly compatible. I would at least expect more of a warning in the schematic. I think your argument makes sense for the Uno, Nano, Mega, but this is a "Pro" model. They have to expect that no everyone will use the Arduino IDE. I learned my lesson, and I'm going off the pin names next to the high density connectors from now on.