Good question, you could theoretically throttle a runaway engine by reducing fuel flow (unlike a piston engine where you can limit air intake). But in 9 out of 10 cases you've already done that by pulling back the power levers. The next step is to cut off the fuel, because the throttles didn't get it under control.
Overspeed protection takes place once everything else has failed. The engine controls have already attempted to throttle down and such. If that doesn't work then overspeed kicks in.
