So, i just noticed that there are only 12 of 4* covers in legendary tokens. I am a bit confused - since when we have this? Is this permanent? How am i suppose to get rest of 4* covers?
Plus one question - i am hearing about “vaulting” and i am not sure what that is…
They’re actually the same thing! Vaulting refers to the fact that only the 12 most recent 4* releases - the ones you see in Legendary Tokens - are available through LTs.
At this point in time, the way you’re supposed to get the rest of the covers for those 4* who have been removed - been “vaulted” - is primarily through bonus heroes, progression rewards, and placement rewards. There are a couple other avenues, but the three I just listed are probably the most reliable.
You can, of course, spend 120 Command Points on a new level in any power you already have rostered at below 5 ranks.
So, briefly said, they made the championing of 4s basically impossible for common players (who are not willing/able to spend thousands of CPs for Legendary tokens before new 4s are removed).
And 5% for Bonus hero or one 4* each 3-7 days from PVE are not very quick ways how to get even one single specific 4* cover…
Well, seems like an another reason to skip 4* part and upgrade + promote 5*s 
Vaulted has been explained above. It’s not something new, disney has been doing it for decades. VHS, DVD and now blurays. It’s how they increase sales when re-released as collectors/diamond/platinum editions. Guess who owns marvel now?