What a waste of $ and resources. Everybody knows that every MO will sign off on a chit saying you can wear boots other than the MK IIIs, so why even bother to do a witch hunt to see if the troop has a chit or not? If he doesn't have a chit when he's persecuted, it takes a trip to the MIR, an interview with the MO and he's got a chit.
How much money does this waste in terms of MOs spending time writing up chits for soldiers feet and how much money is the CF spending on "orthopedically acceptable" footwear. Just have a blanket policy that says that as long as a boot meets certain requirements in terms of color, materials used (ie. no all nylon boots, etc.), minimum ankle height (lets say 8") and has a lace closure, it should be good to go. Continue to issue the Mk III or its replacement, and have regulations that state that the unit commander may dictate their wear for parades, but other than that, individuals may choose to wear what boot works best for them.