As always, please tell me if my assumptions are incorrect.
You seem to be taking this as a sign of front office approach. The NBA and the NHL both have maximum contract terms. They couldn't sign these kinds of deals today, but when it was allowed in the NHL, it is where contracts were going. And of course the NFL doesn't have guaranteed contracts, which means you're well into apples and oranges.
Not all that long ago, the Flyers signed Owen bleeping Tippett to 8 years. He's a fine player, but no one would call him one of the best players on the planet. (Ok, someone would. No one should.)
I'm going to do my best to avoid what you would consider new advanced stats. WAR is also not the almighty, but we'll let that one go for now.
First, Stott is almost 3 years older. That's not a small deal. Without even getting into the quality of the defense he provides, Stott is a 2B and Witt plays the most valuable and expensive defensive position on the field. So we have best athletes in the sport generally funneled into Witt's position and him being a perfectly reasonable choice for the best defender among them. I don't want to disparage Stott because it's not a fair comparison to take a good defensive 2B and compare him to a top flight SS. You wouldn't compare Mickey Morandini and Jimmy Rollins as defenders, right? They exist on completely different planes.
Things I know you like to use like Batting Average and OBP are largely washes, but the difference in power is not small. Stott Slugged .419 to Witt's .495. That kind of difference in power is enough to take you from pretty much a league average hitter to well above it.
What I will use fWAR for is one stat I will steal from Michael Baumann to illustrate just how rare it is for a Shortstop to do what Witt did last year. You may or may not be familiar with wRC+, so the only thing you need to know is that 100 is league average and high is good.
Source:
What Could Keep Gunnar Henderson and Bobby Witt Jr. From Making the Hall of Fame?