This is incorrect. The Mugen clutch will work properly and also mesh properly, I have been using both style of gears for over 12 months. Both Mugen and Kyosho uses 32 pitch gearing so the mesh should be perfect.
I realise the pitch is supposed to be the same, but if you run a mugen pinion gear over a mugen spur, it is better matched if you run a voner pinion over a mugen spur. I run an MTX2, I find the Kyosho pinions wear faster than my MTX ones. My housemate runs a VoneRR and finds the MTX pinions wear faster than his Kyosho pinions on the VoneRR.