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.