Usually not. Would a car dealer do that? "I want to order the sunroof/nav/HID/leather package but I don't want the sunroof."

Keep in mind that if the stock bike has a given part on it then the shop is going to see tons of those parts. It's not unusual to see a stack of 10 or 11 cm stems from a particular line of bikes. Or a slew of saddles. Etc. They're OEM stuff so usually not as desirable, especially things like wheels, bars, stem, seat post, tires, tubes, bar tape, etc.

The only time it may work is if some of the following occurs:
- the part you want is a less desirable one. I swapped out forks - I gave the company a 1 1/8" fork and requested a (soon to be discontinued) 1" fork. They were psyched, I was psyched, it worked out.

- the shop gives you maybe 20% street value or half of wholesale, whichever is lower. "Take off" parts imply lower than normal cost. The shop doesn't have the packaging etc so they wouldn't pay wholesale for it. Why pay wholesale for something that doesn't include normal things like packaging? If they try to sell it at full retail it looks sketchy. Say a wheelset has a street value, meaning a real retail not just MSRP, of $400. If I were a shop I'd give $100 credit and sell it for $150-200. It'll make someone happy to get "take off wheels", aka "used wheels", for half price or less. As a shop I make enough money to cover labor for swapping out tires, cassette, etc, and still cover some of my liability insurance just in case the wheelset disintegrates under the rider.

- you find a customer that wants the stuff you don't want. In one extremely complex transaction I managed to coordinate a purchase of a bike where the frame/fork/headset went to one person (me), the seat post to another, pedals to another, and the build kit to another. It worked out well but it was touch and go. We all got our stuff well below retail and actually well below wholesale. It was like buying a new car but parting it out immediately.