Ac25-7A chg1 (p87) in addressing the requirememnts of 25.111(c)(4) - Configuration Changes - specifically states:
(iii) Drag reduction for a manually feathered propellor is permitted for flight path calculations only after reaching 400ft above the takeoff surface
Therefore if the propellor is NOT feathered AND auto-feather was taken credit for during the performance calculations you will not meet the assumptions of the takeoff flight path calculation.
Because the auto-feather system is thereby rendered quite important (!) another paragraph (241) in the same AC deals with the criteria for an auto-feather system. In particular, the 25.1309 requirements must be met for a 10^-9 failure rate, as failure is deemed to be catastrophic, in combination with an engine failure. Autofeather itself must be 10^-4 or better.
In certification terms you should *never* be presented with the case where an engine fails and auto-feather does no operate. If it does and you get stuck in that <10^-9 case then you probably should think about manually feathering, but chances are you're having a bad day already....