I think I may have just figure out a difference. I went to your mini
baja link and found the model of the engines you use. I looked it up
at small engines warehouse and their was a note that said a spacer is
required on the Intek engines to make the shaft height the same as the
L head engines.

So most likely, the Intek engines shaft, if mounted on a flat surface,
will not accept a standard Comet style clutch, or it may be to close to
the mounting surface.

This is just a guess, but the Intek engine you are using in the mini
bajas looks exactly the same as the Intek 6.5hp engine I am planning on
using. So I don't think their will be any reliablity or performance
issues using this motor in my mini chopper.