You are perfectly right.
The reason to use an extra Arduino (clone) is Prusa Research contantly improving and updating not only the printers firmware, but also firmware of mmu.
So by adding an extra Arduino (Clone) you add only a cost of 3-4€, but making maintence much more easy.
Also an Arduino is not an multitasking system. So checking gpio's, constantly control extruder movement, you have to make shure not to interfeare with the mmu's functions. So it would require much more programming skills.
Using an extra Arduino the code would be much more easy. It's strictly single task.
- Watch rotation of extruder
- If unload detected, send comand to mmu
- Watch rotation of extruder
- If movement (1-5mm) detected, send comand to load and Insert filament 1...5
- If a filament sensor detects Filament Inserates (or mmu tells thad loading ist completed) give signal to the printer.
- Goto 1.
I do not think Prusa will change comands a lot in future (maybe add "success" comand from printer if the printhead filament sensor detects loaded filament - but due to bad relability of prusas sensor I do not think this coming soon). So an "Interface-Arduino" is much simplier than modding mmu-firmware, much more easy to modify.