Official Apple comment:

  The two right-hand ports deliver Thunderbolt 3 functionality, but have reduced PCI Express bandwidth [1]

The full Thunderbolt 3 speed is 40MBPs (use the left-side ports to achieve that).

I can't find any official document which clearly states the speed of the reduced-functionality ports, but Apple also state this:

  All late-2016 MacBook Pro models deliver USB 3.1 Gen 2 (10 Gbps) performance on all Thunderbolt 3 ports [1]

So there may be a 4x speed differential, depending which port you plug into.

[1] https://support.apple.com/en-us/HT207256