The cylinders were not totally dead...just a little weak. Unlikey you would notice it especially if it degraded over time. There is such a small window of time during the compression and power strokes for "leakage" to occur (no matter where it leaks to) that the leak becomes much less apparent to the power the engine is making compared to the relatively long time interval (slow RPM) during a compression check and the constant pressure of a leakdown test. The cylinders were still making compression and the leakdown wasn't totally zero (like with a hole in a piston) so those cylinders were far from dead.
My guess, off the cuff, based on the compression comparisons and leakdown is that the motor might have been down 5 or 10 % on power not 50% or more.
That is not a bad idea on the bent valve thought. Hadn't really considered that a valve might have tagged a piston on a severe overrev at some point. Certainly possible I would guess particularily if you happened to remember such an event. Since the tech mentioned that the intakes seemed to be leaking on the leakdown test it adds more credence to that idea. Usually the valve train on overhead cam engines like the FJR are pretty tolerant for overrevs so it might not be the first thing you would suspect. The engine is protected by the rev limiter on upshifts and missed shifts but if the transmission were downshifted too far at too high a speed the engine can be mechanically overreved and the rev limiter will not be able to prevent it. If I think about it long enough I might change my bet to a bent valve instead of the head gasket.......