I'm not a Thunderbolt expert, but I think the reason is twofold.
Thunderbolt was originally designed as an optical link and optical connectors are highly problematic. Misalign the fiber just a tiny bit and you have considerable losses. So they went with a hybrid design where the converter is in the plugs and the connector is electrical. Later it was changed to all electrical but the design where the connection between the two plugs and the plugs and the devices are two separate things was retained.
The second reason is that this design still makes sense.
With traditional designs the driver in the end device is always a compromise. For example the Ethernet driver has to be able to drive lines up to 100m long, but how many Ethernet lines are really that long?
For Thunderbolt they dis-coupled the physical characteristics of the line driver from the driver in the end device. They basically move all the problems of the physical connection (line length, EMV and so on) form the end device to the cable.
Thunderbolt was originally designed as an optical link and optical connectors are highly problematic. Misalign the fiber just a tiny bit and you have considerable losses. So they went with a hybrid design where the converter is in the plugs and the connector is electrical. Later it was changed to all electrical but the design where the connection between the two plugs and the plugs and the devices are two separate things was retained.
The second reason is that this design still makes sense. With traditional designs the driver in the end device is always a compromise. For example the Ethernet driver has to be able to drive lines up to 100m long, but how many Ethernet lines are really that long? For Thunderbolt they dis-coupled the physical characteristics of the line driver from the driver in the end device. They basically move all the problems of the physical connection (line length, EMV and so on) form the end device to the cable.