Pre-built bikes are usually more economical than custom builds so long as you're not changing any components. As soon as you start "upgrading" parts you are whittling away the value. If you look at a new bike and immediately think to yourself "That bike will be perfect . . . as soon as I change X, Y and Z", you're in trouble. This is especially true if the shop is not doing any kind of exchange/swap or discount on the changed parts.
Swapping parts to get proper fit is one thing. A shop should be willing to work with you on things like cranks and stems if you legitimately need different sizes than what comes on the bike. Most shops have a collection of "take-off" parts from previously swapped out items that they should be able to dig into without incurring any cost. But don't expect a shop to do this for more than one or at most two fit related components without upcharging you. If they have to open a new crankset to swap out the cranks already installed on a bike, expect a charge. They can't resell those take-off cranks that were installed, test ridden and have no packaging for the same price as the new-in-the-box cranks you're getting.
If you're immediately upgrading drivetrain or suspension parts on a new bike because you think you need better performance, you should just build a frame up from scratch. If you have that mindset, chances are nothing on a pre-fab bike will satisfy you. Especially when you start digging into the nitty-gritty of the build. Nearly all pre-built bikes skimp on components that most buyers don't immediately consider like bottom brackets and headsets. You are not getting a Wheels Mfg BB or a King headset off-the-rack. If you're already coveting such parts before you even buy a bike, just do a custom build.
