I have yet to fit the case induction mount or engine to my kart but I suspect it can be made to fit beneath the pod. I have only used the pump around arrangement on my cylinder reed engines with no issue. I plan on buying both the taller mount and the shorter mount to experiment with. The taller mount appears to be about an inch or so taller so I should be able to compare carb angles and exhaust clearances. Maybe Ian will chime in in the mean time.
What pipe are you running? I am using an older Anderson/Viper 2 piece pipe that can rotate around the header and at the center of the 180 deg bend So it should be able to be adjusted to adapt to the engine height change.