In certification-land some assumptions have to be made or we could never fly. Multiple failures are considered where possible, and many systems are designed accordingly. But twins are assumed to always have one engine operative. Not to say both engines can't fail, as we saw with the A 320 that had to ditch after a multiple bird-strike and the ATR 42 that ran out of fuel and also ditched.
Regulations require continued flight performance to be guaranteed if one engine fails at V1 or anytime thereafter during flight, right through to the landing. Autofeather may be required to reduce drag quickly to meet the engine-out climb performance during takeoff or go-around. A delay while pilots manually feathered a windmilling propeller could prove critical. Ergo, the other engine must be protected from anything spurious (like a surge or false signal) that will shut it down at a critical time. Hence autofeather systems lock the 'good' engine out following auto-feather of the bad' engine. Some systems are active at all times, others only switched on for takeoff and switched off when at a safe height where it is considered that pilots would have time to deal with any associated problem.
Regardless of the type of autofeather system, if the pilot had a valid reason to feather the other engine (for example after running out of fuel and needing to glide) it can be done manually.