I think comparing running and cycling is pretty bad honestly. I would not go that route. Equipment basically plays no part in running where as in cycling it obviously does, but as you note, probably less so when going uphill compared to races like Roubaix, Flanders, San Remo and flatter races. Still, I do think its a somewhat worthless measuring stick. I think sticking to cycling is much more appropriate, and instead of compared the times to 90's times where EPO played a big role, the equipment was way worse and the overall professionalism in terms of training, nutrition etc. was laughable, why not compare it to the 10's instead? Thats a lot more comparable, and in hindsight, it looks like the 'cleanest' period of racing from my knowledge.
The start 10's were a lot more believeable than 90's despite Sky. It was also in that period that they had us all believe (which I think, to some extent, was correct) that a lot of factors could be optimized and was being optimized. The bikes are very comparable and the attention to details, altitude camps etc. etc. are somewhat similar to now. So the big question is - what changed?
For my money I think even better optimization and professionalism and simply a once in a generation talent account for a decent amount of the performance enhancement (hard to put percentages on it), but not everything. So what are these guys doing now that they didn't do in 10's?