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I had the same issue using "CaseBottom-_With_Vents" and "Case_Top-Heatsink_Camera__Display_Connector_Cutouts" on the Pi 3. My posts came out to about 2.75mm, which is the size of the pi mounting holes, but I needed a bit more clearance for them to fit in the pi and the top part of the case where the holes were even smaller. I would move the vent on the bottom piece under the chip on the board and the GPIO cutout is too small if you were to attach a 40 pin header. Otherwise everything fits pretty well, and I really like the slim design and easy access to the SD card.