I'm not familiar with REI but aren't they a wide-range sporting goods store like Academy or Dicks? I wouldn't expect anything from a store like that. If they have a dedicated bike shop within their store, then maybe.

I know that a stand-alone LBS will do quite a bit. Every bike I've bought has been modified to some extent (handlebar swap, stem swap, saddle swap, etc..) and there was no extra charge. Part of their service is making sure the bike fits you and often that means new components. I would also not be surprised if there was an upcharge if they didn't have anything they could swap without losing money but I'm guessing they have tons of spare parts in the back.

ETA: I just re-read your post and you are wanting to upgrade. I would definately expect a charge for that although it might just be a discounted price due to your "trade-ins" or they might charge labor. It probably varies from store to store. The changes I was referencing for same-level components for better fit.