If a bike I order comes with certain components that I don't want should bike shop swap them?
Giving me wholesale value on component I don't need and selling me components I do need

So if bike comes with 11-28 and I want 12-25 or mid compact cranks and I want standard or size of handlebars and cranks are too big for me

What about wheels?

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.

The components I want are not undesirable (I don't think)
They could always sell a 11-28 Ultegra cassette
Think they could always sell 42cm handlebar (maybe to someone who's stock bike comes with too narrow or wide a handlebar)
The cranks might be more of an issue
Why don't more bike companies let you pick what you want then before shipping the bike?
Using the car analogy if I don't want the nav/sunroof/leather I don't order the car with it
Seems to me that it should not be a big deal to do that
Otherwise I am spending thousands on a bike plus having to purchase new handlebars, cranks, cassettes (and left with ones I won't ever use from the way the bike was delivered)

when I bought my pedal force, I got to choose everything. got exactly the stuff I wanted.

By "undesirable" I'm not saying "not good", just "not immediately salable" in that environment. 42 cm bars are super common, ditto 11-28 cassettes. A shop will only take extras of such parts if it's at a blow out price. To give you an idea it's not uncommon to buy a take-off bar or stem for $5 or $10, even if the "retail" on the same part in a box (or in a more unusual size) is $50-100. Take off tires are basically giveaways. The last take-off part I dealt with was a carbon stem. It was the stock size for my frame and I had a hard time giving it away, for real. Even an 11-28 has to wait for a service demand, i.e. a bike that needs a new cassette, or a customer that understands what they're getting.

For example if I was a shop and I already had an 11-28 cassette in stock then I wouldn't want to give full wholesale credit to a customer that doesn't want the 11-28 that came on his bike (and on dozens of other bikes I already stock).

As far as the "picking out the components" that's a different story. You can do it but you should be prepared for a lot of decisions and trading something (price, knowledge, convenience) to get the parts you want. I know that the big online stores like Excel and Competitive Cyclist allow you to do some of that picking. So does Neuvation. You're not going to get a Trek or similar to do a custom bike program at the lower levels.

Bike companies have to commit to purchasing x amount of stuff. If they don't know they can sell it then they won't order it. I firmly believe that there are product managers that will over-purchase in order to get good prices and then grey market the extra build kits at blow out prices. When I was a shop I'd see build kits that were so cheap that I could buy a frame at retail, add a build kit at retail, and still be 10-20% below the retail of a similar bike from a bike company.

Ultimately if there is such a demand for custom bike kits then someone (you?) could make money providing such an opportunity. The reality is that it's not a good way to try and make money. The limited number of bike companies that offer this is evidence, at least at some level.

Depends on the shop.. your relationship with them and how likely they are to resell the take-offs in a reasonable amount of time. I have one shop that will trade out just about any component on a new bike for fair market value toward a replacement. In fact, when I bought my Roubaix, they bought the wheels outright for $400 since I was having some built elsewhere. Not all shops do this, so ask them up front.

I have great relationship with them and they have been great to me over the years. This is first time I did fitting before getting bike and cranks, handlebars and cassette are not good for me. But the geometry is spot on. I would think a 42cm handlebar and 11-28 cassette that come with the Specialized Tarmac or Venge will not be hard for them to resell

Sounds like you know exactly who to talk to then.... call them up or stop in.