PNaCl is just like module that can be executed in C/C++ Runtime which resulting greater performance than javascript that running over web runtime.
Not sure about the exact answer, but this is my understanding. Because of the SEF is more likely system object interface then it should compiled with firmware. And yes, i agree with you the SEF is "lower" than the PNaCl but i think that's impossible for us to create our own SEF plugin except Samsung releasing the source code and method to flash the firmware like android device.
System Runtime | <==> Sandboxed Runtime <==> PNaCl
| /\
| ||
| \/
[SEF Object] <======================> Web Runtime <==> Javascript