I've had the same reaction to the possibility of diaphragm air leaks. However . . . I thought the effect was the opposite from the one you describe.
Without air-tight seal and full vacuum, I thought, the slide and needle would not rise as they should in response to the throttle valve opening. Since the needle cannot uncover the main jet adequately under that circumstance, the mixture would be fuel-lean, since fuel flow through the main/needle jets would be compromised (insufficient needle lift).
I thought this theory was validated, when I found an engine with a carburetor diaphragm air leak that would run only with the starting enricher fully open, fuel-enriching the mixture to compensate for the inadequate fuel flow from the "too-low" needle excursion.
Summarizing, I thought the effect of a diaphragm air leak was a fuel-lean mixture, not a fuel-rich one.
My theory/conjecture only; if in error, I appreciate any correction/alternate explanation.
BTW; Alpheus has departed the KLR fold; is now a full-up Harley man! A function, somewhat, of his longer commute into his "day job" from his new lake community home. His expertise on Keihin CV carburetors will not go entirely to waste, depending upon the Harley models whose company he keeps!
Take the fuel tank and air intake duct off of your Bayou 300. (I think I remember you said you own one?) Easier to see than the KLR650.
Remove the carb top. Insert a bristle from a broom, to create an vacuum leak, reinstall carb top. Start the engine and try to raise the RPM, while holding a business card near the bell mouth of the carb. Note the 'spit-back' of raw fuel. I could be incorrect. I've never done the business card trick!
The Non-rising slide acts as a manual choke plate. The mid-range jet NEEDLE does Not completely seal the mid-range needle JET.
Therefore the engine should be pulling raw fuel from the idle mixture screw, the 3 low speed by-pass holes and the mid-range Needle/Jet.