Negative torque protection is usually only provided if the pilot does not retard the power lever. If the power lever is retarded to flight idle, most props will go to a high drag state - not beta or reverse, but still enough to cause control problems at low speed. At a critical time immediately after V1, if the engine bangs, surges, farts or explodes into a thousand pieces, locking out the autofeather by closing the power lever all the way to flight idle at low altitude is a bad idea.
The entire takeoff performance is predicated on the autofeather taking care of any failure at or soon after V1.
Autofeather systems are extremely reliable, so much so that some operators no longer require pilots to conduct manual feather drills immediately after takeoff.
The history books are littered with accidents caused by pilots losing control due to windmilling props.
Unless your Company specifically preaches another doctrine or the FCOM clearly states something to the contrary, for engine malfunctions after take-off, I would not be retarding to flight idle below 400 feet or below V2 plus 10 knots.