Don't get me wrong here because I think 80% of your post is accurate, but I have to disagree with teams being penalized. I think they get penalized when they overpay for their own players simply because they drafted them and they sell jerseys. Diggs is a great example of that. They have a player here that they spent a 2nd round pick on and now have maybe the most valuable CB in the league given his performance/ceiling/contract. They don't have to sign him, and could easily cash in on that value and get a pile of assets and cap freedom coming back their way, much like KC did with Tyreek Hill last offseason.
Prioritizing the draft is an excellent thing, and I love how well the Cowboys have drafted over the last decade or so. The problem is after you still have assets that fluctuate in value and on occasion you have to be willing to cash in on some of those assets. Instead Jerry tends to sell players at their lowest value like Amari Cooper.
I agree, but this is based on the reality that comes with the CAP and free agency. I am sure, for example, teams would prefer to keep the all-pro players they drafted rather than see them leave for free agency. It is just not possible today so teams prioritize, and even then may lose players they hoped to keep.
I can compound this by saying that teams that are bad at drafting wind up not having to pay top dollar to retain the layers they drafted. So they have CAP room to sign away the better players someone else drafted and can't afford.
This system works for the league because they want parity. Bad teams draft first. Good teams draft last. Good players are more expensive than bad one so teams that draft well have to give up some of their talent to the teams that draft poorly.
Overpaying players is a problem specific to the front offices of some teams.