I mounted the SSD with standoffs on the opposite side of the heatsink. That exposes the uSD slot, GPIO header and allows the board to be protected by a modified $10 RPi 3 case w/cooling fan.
Some filing was necessary to provide clearances for OTG switch, RTC header, & USB-c connector. The bottom of the RPi 3 case separates the SSD card from the heatsink and adapts RPI mounting holes to SSD standoffs.
The provided pillars will interfere with the RPi case, so I needed to purchase 2 x 2.5mm X 12mm long flathead screws from the local Ace Hardware ($.74) to pass through the board, thread into the M.2 adapter, and thread into the heatsink (last image, final mod).
After taking the photo, I found that a few nylon washers in between the mainboard and M.2 shim provides the necessary clearance needed for the eMMC module. Otherwise, allow a few threads to show on the mounting screws (standoffs), by not completely tightening the shim down, prior to installing the heatsink. Consider the mounting screw as a means to adjust the distance.
Hope this helps.
Note: Photos show the original ver 1.2 M.2 extender board. The new ver 1.4 extender board has the M.2 connector underneath the extender board.
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