The 13" uses processors with 12 PCI-e lanes, and Thunderbolt 3 needs four lanes per port for full bandwidth. Hence two run at full speed; four lanes each for eight lanes. The other two have to make do with two each so are slower.
The 15"s' processors have 16 lanes so can run all four ports at full speed.
Full discussion here:
https://www.macrumors.com/2016/10/28/macbook-pro-tb3-reduced-pci-express-bandwidth/
I expect a mod will close this thread.