As I see it, Spanos took a bullet for the NFL. Neither He, Kroenke or the NFL wanted to see the Raiders, or Raider fans, in Stan's new stadium. Only way to do that was for the Chargers to block the Raiders move. And if it resulted in San Diego building a new stadium instead, then it's win-win.
That aside, and I admit ignorance in regards to anti-trust laws etc., what's to keep the NFL from building San Diego a stadium and renting it to the Chargers? If necessary, they could create a spin-off NFL Stadium Development corporation separate from the league offices. There are enough rich owners they could mass the necessary capital and share in the potential profits.
Pursuing that thought, could Kroenke himself (Of a Kroenke umbrella company) build a new stadium in San Diego and then rent it back to the Chargers? (Or put it in his son's name like he did his other sports assets.)