The 20km Individual is the longest distance they cover on the World Cup outside of the one or two 50ks a year that we get as an anomaly.That's not the right comparison you make.
Top 10 in the mass start were separated by 1 minute. Top 10 in the sprint by less than 30 seconds.
Also, how would you change to bonus system in sprints?
You can't give time bonuses only for the first 3 as you punish the others making them do an extra effort for nothing. And you should somehow reward everyone who passed the qualification as they still do an extra effort
Also, you're other comparison is way out of line. None of the 3 you mentioned is even top 50 on the hard mountain stages. In comparison to the likes Diggins and Klaebo, they are comfortably top 10 and actual favourites for some distance races.
Valverde, if you ask me, is decent comparison to both and he podiumed all the GTs and won one.
If we compare distance races to hard GC stages and sprints to TTs, in cycling you don't see the likes of Mas or Cancellara dominate GC's, you're looking for all-rounders (or rarely extremely gifted climbers) the same goes to TdS. You don't get the likes of Pellegrino or Holund dominate, you get all-rounders (Diggins, Klaebo, Boergen, Bolshunov, Cologna...) and rarely extremely gifted distance skiers (like Bauer and Johaug) win.
I mean, all the bad things aside, Peter Northug was really all-around skier and he won only one TdS.
When I think about it, the biggest problem aren't the big sprint bonuses, but the presence of 2 mass starts and one pursuit instead of one more 15-20 km individual race.
Imagine giving out the same time bonus for sprint wins that you give for the spread of the top 10 in a 50km ITT.
Yes, Valverde is a good comparison for somebody like Diggins, I'd agree. But how many Grand Tour bunch sprints has he won? Like, actual sprints. The kind of sprints Valverde wins are comparable to the 15k mass start that Diggins won on stage 2, and got... no bonus seconds for.
And how would I delegate it? 5 seconds bonus for heats, 10 seconds bonus for semi-final, 30-25-20-16-14-12 for finalists. Definitely nothing more. Make it so that if you get through to the sprint you have to decide whether or not it's worth pushing it, at the moment some of the GC skiers who know they aren't getting anywhere in a sprint are happy just to take the bird in the hand by getting the free time gifted to them for being there. Just reaching the semi-final of a sprint is not enough to merit the same value as coming top 5 in a 20k individual start, especially when sometimes it's just a matter of not falling over in some of the demolition derby sprints. And look at the women's Tour today - there's what, 42 remaining athletes? So being in the top 30 is hardly some kind of achievement worthy of a whole swathe of bonus time.
I mean, even then I think I'm being pretty generous. After all, Klæbo won today's sprint with a time of 2'35 after a qualification of 2'34. He will have had to do the course four times for a total of ~10'30 time spent racing. In the 20k Individual Amundsen won with a time of 44'05 - more than four times as long. Klæbo gained 52" over Amundsen in the freestyle sprint in Toblach, despite that Amundsen actually set a faster time to be eliminated from QF 2 than Klæbo set to win QF 1. Amundsen has come 3" behind Klæbo over 15k, beaten him by 46 seconds in a 20k, beaten him by 5 seconds in a 15k (although that counted as losing 40 seconds or so because of the pursuit)... and was a minute and a half behind him on the GC after four stages despite actually skiing faster than Klæbo in the stage he lost almost all of that time.
So Amundsen lost 3" in sprint quali on day 1, 3" on day 2, gained 46 seconds on day 3 and lost 41 of those back on day 4. Totalling a difference of 1 second's actual skiing difference between the two. The rest of that minute and a half gap before today was time bonuses given to Klæbo for sprints and intermediates. That's just absurdly disproportionate to my mind.