First off, the salary cap is real. Every team has the same amount of cap room. It is the great equalizer.
Every team's goal should be to use the available cap dollars, most judiciously, to assemble the greatest amount of team talent, and depth, to win a SB. Every team should also maximize every non-cap area (coaching) to get the most out of the talent you have on your team.
Now, on to the meat of my post. The Cowboys allocation of cap dollars, on individual contracts is really off base. Lets say you have a guy who is the top QB in the NFL. You would expect that at the end of his rookie contract, the #1 Qb is going to probably be the highest paid at his position. It doesn't matter if its Tom Brady, or Rodgers, or whoever your team evaluates is the best player at his position. That guy, should arguably set the QB market.
If you have a franchise QB (in this case, its Dak) you may want to keep Dak, because there are no perceived acceptable substitutes but you have to decide (realistically) how does my QB compare to the best QB in the NFL (and his contract). Lets say that Dak is 70 percent of the QB as QB#1. He should, theoretically sign for 70% of QB#1's salary. Anything more than that really hamstrings you because you are poorly allocating cap dollars to a lesser player.
Tank is another example of that. Tank is arguably HALF as good as the top player at his position, and yet his salary is commensurate with the very top players at his position. I can understand wanting to overpay a QB (to some degree) because you can't win without a good one, but you can't overpay so much that you can't put better talent around your QB to elevate his level of play.
You also have to consider WHY a player produces. Witten had a ton of catches, but that was in part due to the fact that opposing teams WANTED Witten to get catches because his ability to hurt them was close to zero, except in very short yardage situations. A player like that shouldn't get rewarded for lots of catches, because in almost every situation, him catching the ball is hurting you more than it is helping you.
Shultz got a lot of catches last year. He seems to have a knack for finding seams and getting open. But is he worth a franchise tag? Probably not.
Would you rather have Bobby Wagner (assuming he is healthy and can still play at a high level) and a draft pick at TE, or Dalton Schultz and a draft pick at linebacker? Who would be more productive? You might say, well Wagner is done. Maybe he is. But really good impactful players hit free agency most every year due to the cap. You want to be able to sign these difference makers. What you don't want is the Tank/Zeke/Schultz contracts prohibiting that.
The salary cap is about opportunity cost. The Cowboys are giving up too much for too little.
The Cowboys also really missed out on another opportunity. We should have offered to extend Wilson last year for peanuts. He would likely have taken a 2 or 3 year deal for security. Little contracts like those make all the difference in the world.