Thunderbolt can kinda-sorta mimic PCIe, but it needs to chop up the PCIe signal into smaller packets, transmit them and then put them back together and this introduces a big jump in latency, even when bandwidth can be rather high.
For many applications this isn't a big deal, but for others it causes major problems (gaming being the big one, but really anything that's latency sensitive is going to suffer a lot).
Thunderbolt is external PCIe.