There are plenty of custom bike builders out there that allow you to pick and choose the component spec. Example, Rivendell. Trek is offering a similar service at their high end.

But, in those situations, you are generally paying full retail for each bike part, with maybe a slight discount for the bike maker's preferred build kits.

For mass-produced bikes, you pay closer to wholesale for those components because the bike maker orders them by the truckload.

It sounds like you want custom-bike choices at production-bike prices, and that's not going to happen. That's why most manufacturers offer different build kits for each model, so you can retain some selection.

That's why it's popular to buy a production bike, strip it for its component kit, and sell the frame. You get a full build at a cheap price for whatever frame you choose.