A little update to this: I got the Samtec sample, but as I suspected the connector body is too wide so without literally cutting corners (quite doable, but cumbersome) it would not fit inside the throat of my capsule. Another issue was that the footprint also is wider with the legs extending, so I would get into trouble with space on the interface board. As the connector also is 2 mm deeper I suspect I would need longer fingers, and that again would prevent my device to fit in the capsule. The connector although listed as an 8-position connector only had 7 positions with pins, I guess the key is counted as one position. (I could still have worked around this).
I tried out the idea of drilling a hole for a key and it was quite successful. If the interface was to go into larger volume production, it would not be difficult to make a jig for the drilling. As key I used a piece of 0.9 mm mono filament (fishing line) that I had floating around, and it basically locked itself in place as the cuts when performed a bit slowly would widen the ends (attached image). One just has to remember to insert it after reflowing the board... Thanks again for the exchange of ideas in this thread.