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.

1. Watch rotation of extruder
2. If unload detected, send comand to mmu
3. Watch rotation of extruder
4. If movement (1-5mm) detected, send comand to load and Insert filament 1...5
5. If a filament sensor detects Filament Inserates (or mmu tells thad loading ist completed) give signal to the printer.
6. 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.

@fma I think its even more simple, if you use an arduino.
Simply connect the arduino to DIR and STEP of the extruder driver. Let the Arduino count steps every time DIR is in backwards direction (reset counter if a step is done forward). If the number of steps exeed a certain number, obviously its not retraction but filament unload.
So the command to change filament is unload filament.
The arduino than sends the command to retract the filament into the MMU to the controller of the MMU.

To select the new filament, let the extruder step into forward direction for 1-5 mm. This does effectly nothing, as the extruder is empty. But the arduino can interpret this as "I want filament 1-5", so command in gcode would be extract 1mm filament to select filament one. The Arduino than sends the code for Filament selection to the MMU.

Than let wait for Filament change completed by the MMU. Than the arduino triggers a gpio on the duet; in gcode its an m226 to wait for this pin. Than start loading (if your printer has autoload, this is notneeded, simply use m600 insted).

This technique may work not only with a Duet, but with nearly any 3d fdm-printer, even the cheapest ones - if you dont have access to dir/step signals, use an optical encoder on the extruder-motor, if you do not have a free gpio or autoload-function, set a relais in parallel to the O.K.-Button and use m600.

Only think is calibration. You may do that by terminal via Arduino to the mmu.