Are all the ports on 2016 MacBook Pro 13" the same speed?
As it turns out, there is a support document published by Apple that directly answers my question:


  Late-2016 MacBook Pro models vary slightly in the data speeds they
  provide to each Thunderbolt 3 port.
  
  MacBook Pro (15-inch, Late 2016) delivers full Thunderbolt 3
  performance on all four ports.
  
  MacBook Pro (13-inch, Late 2016, Four Thunderbolt 3 Ports) supports Thunderbolt 3 at full performance using the two left-hand ports. The
  two right-hand ports deliver Thunderbolt 3 functionality, but have
  reduced PCI Express bandwidth.
  
  MacBook Pro (13-inch, Late 2016, Two Thunderbolt 3 Ports) delivers
  full Thunderbolt 3 performance on both ports.


Therefore based on this, I will use the left-hand ports for my high bandwidth peripherals.