It'll really depend on the store. During the holidays, your chances are both higher and lower. Stock moves much faster, so you may find a manager willing to put an order in for a case if you can convince them it'll sell. Then again, as busy as it is, they may not have time to cater to such a request.
Typically if what you are looking for is part of an assortment, that kind of stuff is on auto order and whatever the warehouse has is what is shipped. So say you wanted a Diamond Rose, they probably couldn't order that specific case. But if that is the current assortment shipping to stores, if you ask nicely and be polite, they may just order an extra case and give you a call when it comes in. I've gotten to know employees at Target and of all places the Star Trader in Disneyland (I collect Star Wars figures too), and if I ask nicely they would check in the back to see if they had anything. As long as they know you're not a toy scalper and you're polite, you can usually fine someplace that'll help you out.
Good luck in your endeavor!