Rob Van Dam's contract structure of working 90 days and then getting time off was something he and Triple H came up with according to PWInsider.com. Vince McMahon did approve when it was pitched to him.
RVD has other projects going on he wants to devote time to which is one reason he doesn't want to work for extended periods of time. He is allowed to work with other wrestling companies while taking time off but can't appear on their television or DVD's.
WWE creative is hoping to have RVD back for Royal Rumble and book him through Extreme Rules. This would be longer than 90 days but the company is confident they will have RVD through at least WrestleMania.