If I am Dak, I ask for the entire house and if I don't receive it walk.
Like you said, it is clear that Dak was the reason the team looked decent and his leadership (which can't be measured) kept the team in check. Jerry played a dangerous game that is ending up in Dak's favor even though he got injured.
I mean... it kinda worked out for Jerry though.
On the surface, you'd think Dak's got them over a barrel.
But Dallas has three key things working for them:
1. A player coming off a brutal injury, with pretty much no possibility of showcasing that he's recovered prior to either side needing to make a decision on his future with the team.
2. What is very much shaping up as a top 5 draft pick. Jerry can dangle that in front of Dak as leverage for as long as he needs to, and it'll probably help. They can basically tell the world that they can get a good QB in the draft if they so choose.
3. A declining salary cap in the year when Dak is a FA.
The third item isn't necessarily an issue, depending on the structure of the deal, but keep in mind that a lower salary cap is a reflection of lower revenue, and cash is cash in the NFL. Owners coming off revenue declines may not be as interested to spend large piles of cash on players in the offseason. And if you're signing Dak, its going to cost a LOT of cash up front.