If you need to time your peak so specifically you get dropped for 2 weeks and are completely at the mercy of your rivals aggression level, then you're not indisputably the best climber.
Like his one best performance in that Tour was putting like a minute into Kruijswijk who was letting his own domestique set the pace. Day after he got dropped again on Val Thorens by the way.
He was lucky Froome had his crash. He was lucky Thomas bottled his peak as hard as he did. He was lucky Jumbo prioritized Groenewegen over Roglic that year. And he was lucky with the Pinot freak injury. And he still won by barely 1'30 over Steven Kruijswijk.
There were like 5 reasons to question he would win the Tour 5 times, and the only reason to think he would do it was that he was super young.
Dropped for 2 weeks, at the mercy of your rivals aggression level?
He lost 9" to Thomas on la Planche des Belles Filles.
After the ITT he was 2'52" behind Alaphilippe. 1'26" behind Thomas, first of the real GC guys.
He was 5th, losing all of 8" to Pinot on the Tourmalet
He was 4th of GC guys, 5th of the stage to Foix, 18" behind Pinot and Landa
He gained 32" to Valloire. On everybody in GC. Up to second, 1'30" behind Alaphilippe
Then destroyed everybody on the Col de l'Iseran, looking to put more time in on the final climb.
Yours is a very weird reading of what happened in the first 2 weeks.. .completely at the mercy of his rivals... After stage 15 he was the third best climber in the race, having lost 33" to Pinot and 12" to Landa in the mountains.
AS for Krujiswijk, well, has it occured to anybody that Kruijswijk was a pretty good rider that could very well have won the Giro 16 if not crashing?
In hindsight, yes, unlikely that Bernal could have beaten Vingegaard and Pogacar. But a Bernal without his back problems, without his crash normally would easily end up on the podium in 20, 21, 22, 23, with a second place in 21 and 23 very possible too. But in the end he would regularly get destroyed in the TTs, while not bad, clearly not at the level of Vingegaard and Pogacar. But there's nothing to indicate that he would have been regularly dropped by those 2 in the mountains.
As for Quintana vs Bernal. Quintana was in the wrong time, had Froome against him, Bernal didn't. That doesn't make Quintana stronger than Bernal either though. 2 very strong young riders, that faded earlier than expected, although for very different reasons.