The current BFL chip has an on die temperature sensor, they just aren't using it. If I had to guess it's a cost issue; it's cheaper to toss a couple 20 cent temperature sensors on the board that it is to properly mux and read 16 temperature diodes.
My guess is that the reason to use external sensors is that the internal ones are too noisy and very inaccurate. The cost is indirect: they can't afford to design the de-noising hardware/software and can't afford to properly characterize and calibrate the internal sensors.
It is actually quite common problem: many SoC chips have on-die temperature sensors but use external ones because otherwise they wouldn't meet the time-to-market goals. This includes even very-well capitalized entities which already have the methodology and the tools available.
I agree, I also think this is the reason why they didn't use this pins.
Anyhow, this pins are not connected on BFL's PCB designs. At least not from reading the jala schematics. I guess the single-sc design is not different in this point.
So no (easy) way to use them in existing BFL products.
@MrTeal: Did you use this pins in your design?
Who ultimately makes the decision whether a certain feature you designed is used or not?