True supply and demand coming out of college would be a bidding system for the "best" players. The player's comp on a rookie contract is artificially constrained by the rookie pool, which new players to the NFL did not collectively bargain as part of the NFLPA, because they didn't belong to it at the time.
Then, the NFL mandates that contracts are for four years (with a fifth year option), which is fine for a wideout or offensive lineman who are still on the upswing of their peak and likely have their best years ahead of them on their second contract. Running backs come into the NFL very near their peak, which is when their compensation is constrained by a structural factor, not supply and demand.
You make a good point that RBs are uniquely screwed by the rookie contract structure of the CBA, thus RBs on rookie contracts are a bargain for teams, then get screwed on second contracts since we all know their best years are usually behind them after 4-5 years.
If RBs provide so much value vs. their cap hit, teams should covet them in the draft like QBs. Yet aside from a couple outliers most years, they don't.
The couple of standout RBs on rookie contracts each season have a tough time ever receiving compensation commensurate with their value, unlike say QBs who are just coming into their prime by the time their rookie contracts are ending.
Not sure what could be done about it in the CBA - mandating higher rookie salaries or shorter first contacts for RBs would push them even farther down draft boards, and make it tougher for the non-superstars to catch on with a team at all.
So maybe it just comes back to supply and demand at a position that's been devalued by rule changes over the years.
The top 3 RBs last year helped their teams to losing records, and the top 7 had one playoff win among them (Barkley).
On the other hand, the top 7 WRs and 13 of the top 16 were on teams with winning records or playoff teams, and Kirk, while surely overpaid, was one of them.
(I suspect the increasing supply of good WRs will eventually cool off the market for that position.)