The OP still refuses to give an airplane or engine type, or tell us whether this is a real or FlightSim question...
If the autothrottles are not keeping up with external influences, whether it be mountain wave, turbulence, wind shear, or something else, then the simple answer is to take over manually, regardless of what someone might "prefer". If the conditions are so extreme that the autothrottles command IDLE as he posited, then "loss of separation" is not likely an immediate factor. If you are pushing the red line AND climbing in a wave, spool-up time should also not be an immediate factor unless you got into a "coffin corner" situation in the first place, whether by bad planning or extreme bad luck.
I do agree with misd-agin that speedbrakes are preferable to excessive thrust reduction at high altitude. However, the question appeared to be regarding the ability to control the thrust. Anyone who "prefers" to use autothrottles to control thrust when a described extreme/limiting/edge-of-the-envelope situation exists is not someone I'd "prefer" to fly with.