I don't think the amount of TT mileage had such a big effect on who was a super responder and who wasn't. The hardest mountain stages were also much harder then.1991 Tour: 135km of ITT, 36km of TTT
1992 Tour: 137km of ITT, 64km of TTT
1993 Tour: 118km of ITT, 81km of TTT
1994 Tour: 119km of ITT, 67km of TTT
1995 Tour: 108km of ITT, 67km of TTT
1996 Tour: 103km of ITT
1997 Tour: 125km of ITT
1998 Tour: 116km of ITT
1999 Tour: 121km of ITT
2000 Tour: 75km of ITT, 70km of TTT
1991 Giro: 116km of ITT
1992 Giro: 112km of ITT
1993 Giro: 92km of ITT
1994 Giro: 86km of ITT
1995 Giro: 104km of ITT
1996 Giro: 62km of ITT
1997 Giro: 58km of ITT
1998 Giro: 82km of ITT
1999 Giro: 77km of ITT
2000 Giro: 82km of ITT
1991 Vuelta: 124km of ITT, 49km of TTT
1992 Vuelta: 97km of ITT, 33km of TTT
1993 Vuelta: 116km of ITT
1994 Vuelta: 102km of ITT
1995 Vuelta: 100km of ITT
1996 Vuelta: 90km of ITT
1997 Vuelta: 78km of ITT
1998 Vuelta: 79km of ITT
1999 Vuelta: 98km of ITT
2000 Vuelta: 89km of ITT
This is probably your biggest culprit. Interesting to note how the Giro went a whole decade without a TTT and were actually the ones with the least TT mileage, reducing down to only one long TT in the mid 90s, possibly with the hope of keeping crowd-pleasers like Pantani in the mix more than they could be in the Tour. The Vuelta in 1991 has two TTTs (one in trios and one as a full team), two long ITTs and an MTT. All of those tour TTT mileages are from a single stage, they don't have an example like the 1991 Vuelta with two TTTs, so an 81km TTT being in the repertoire absolutely was part of the sport back then. Notice how the Tour scales back ITT mileage and replaces it with TTT mileage from 1993 to 1995 to try to engineer closer competition to Indurain, but without drastically altering the balance - suspect they had little problem with Indurain winning but wanted to foster a closer competition; of course he also won the 1992 and 1993 Giri, the latter of which had reduced ITT mileage, notwithstanding that part of that was the Sestriere TT which finished with the long uphill drag and eventually climb. Similarly the 1994 Tour includes that 47,5km Morzine TT that went over a couple of climbs which Piotrs Ugrumovs went nuts on. This type of mixed TT is pretty uncommon nowadays, certainly over that kind of full distance. We get a few TTs like the mini-MTT to Megève a few years back, but I'm thinking something more like Sestri Levante in the 2009 Giro as the last example I can recall off the top of my head of this type of TT which is not an MTT but includes a wide array of terrain and has mountains but not as a defining feature.
In the 90s, some of the craziest climbing performances were done by guys over 70 or even close to 80kg. And yes, that's also unquestionably to some degree down to better gear and thus flats in the peloton becoming much easier.