Board specific pinout configuration conflict resolver

Is there a way to set the mcu pinouts based on constraints imposed by the physical wiring of the board?

[Gui extension]

I'm dreaming of having the ability to add custom "rectangles" and "lines" to the pinout view which represent the wiring on the board.

[text based]

On the other hand, a solution based on text files would work, too. Is it advisable to write an application which generates files akin to the ones in /STM32CubeMX/db/plugins/boardmanager/ ?