The problem with Thunderbolt is that it's essentially PCI-Express, so much closer to the hardware & kernel and a malfunction is more likely to lead to a crash,

The problem with Thunderbolt is that it's essentially PCI-Express, so much closer to the hardware & kernel and a malfunction is more likely to lead to a crash, especially considering hot-pluggable PCI-E is relatively new and not as battle-tested. USB in contrast has been built from the ground up to be hot-pluggable and there's been decades of real-world testing with terrible manufacturers and people not "safely removing" devices, so most of the bugs would've been ironed out. Your device may malfunction, but it's unlikely to lead to a full system crash.