NFL gave leeway on how teams could manipulate their rosters.
Niners took a gamble and lost.
So basically, the NFL is saying.. well.. we tried to make it your decision to control your roster... now because of your idiocy which in turn makes the NFL look bad because you didn't activate 3 QBs when you had the full power to do so... we will now step in and have more control over your roster because of your mistake.
These same people are probably like.. I want less central control and more power to teams... but then they screw up and now Daddy or Mommy need to step in and set some rules. Way to go Niners.