1) Thunderbolt dock requires Thunderbolt port, while USB-C dock works with just much more common USB-C + DP alternate mode port.
2) USB-C docks just work, while Thunderbolt docks often require magic steps to enable them (like changing options in BIOS).
3) USB-C is relatively secure, while PCIe is just a gaping security hole unless IOMMU is used and configured. I am not sure how common that is.