’ Once again, I take the opportunity to say that I would never use a board like the Raspberry PI to implement a real product. For many reasons, including but not limited to reliability, in my opinion, these boards are OK to make Proof of concepts (PoC) or** hobbyist **projects only.’
hmmm … I disagree 
your (nice) article describes a SINGLE CHANNEL gateway, that’s the reason your missing packets.
SINGLE CHANNEL gateways are only for test purposes and study because they are not LoRaWAN compliant.
To ‘fix’ the missing packets you have to edit the channels in your LMIC node (from 8 to 1 ch - same ch as gateway)
or see RPI + RAK for a full diy 8 ch gateway