You are correct, technically you can update and address each individual pixel, but this is only in the MD_MAX72xx display buffer. The display update of that pixel occurs because the entire display is re-sent to the MAX72xx chips. The fact you can't tell this is happening is a testament to the speed of the update.
This negates the purpose of just updating a section of the display (used with the LCD display) as there is no 'saving' of any sort. In fact, probably complicates the code somewhat compared to just a whole screen redraw.