The gearing is a real possibility.
And I think I see where you are going with the idea of focusing on the average.
However, when I look at the power file, the ride looks like a series of 350w intervals. Normalized power is not outrageous (that is, not far off of target power for L3 tempo rides.) But the power distribution is what looks very time inefficient.
So, for example, in a 2.5 hour ride the other day, average power was 159 (which is fine for an endurance ride), but normalized power was 222. Now, that would be almost perfect for a tempo ride. But I only spent 26% of the 2.5 hours in that power zone. Almost 30% of the ride was coasting, and the rest was either over threshold or way over threshold.
And I think I understand your pt. about heart rate, too -- you seem to be saying that the effect of a super-threshold effort doesn't set in until after HR exceeds LTHR, which comes only in the second half of a 4 min effort, and that ends up being a relatively small part of the whole ride. (Maybe I misunderstand this.) But I'm not sure I agree that "the real stress happens after the first 2 mins." I think this may be confusing HR and power. Just because your HR hasn't (yet) reached super LT does not mean you are not putting out super-threshold power and therefore experiencing the physiological effects of a super-threshold effort right from the start. I would think any time spent at super-threshold power would count as at super threshold power in terms of physiological damage. I suppose the depletion is not instantaneous, but clearly 1 min intervals at 425w, during most of which HR does not go super LT, "hurt" more than the only the last ~20 secs during which HR is super threshold. I take it that is why 12 x 1min @ 425w is enough for a day's workout even though only, say, a total of 4 mins is spent above LTHR.
Now clearly very different energy systems are at work in sub- and super- threshold efforts. But that seems to be just my concern. I cannot think how to keep workouts at sub-threshold levels in order to train those energy systems, even if the super threshold efforts are relatively short. They add a lot of physiological stress I don't want -- and, more importantly, the wrong kind.
I can't be the only person who has to train in this kind of hilly terrain.