A good analogy for building a web site is that it's like building a house. If you were to ask a contractor how much would it cost me to build a custom house, the contractor would probably have a bunch of questions for you. For example, what kind of house do you want? A rambler, colonial, detached, row house, split-level? That would be a high-level question.
Getting down to the nitty-gritty, the contractor might then ask you what kind of layout did you have in mind? How many bedrooms? Where will the kitchen go, etc? Then, the contractor might get pretty specific, such as what kind of cabinets do you want in the kitchen, and what finishes do you want throughout the house... as you can see, this can get pretty complicated. Then, there might be some specialty features you'd like to request, such as a swimming pool, landscaping, etc. Those are all extras. Also, the type of materials used, and appliances installed can make a difference as well.
It follows that a good amount of planning should go into the project to ensure that you get exactly what you want, and that all the work can be completed within your desired timeframe. Then again, you could always go with the builder's generic offerings, such as preconfigured layouts, with predetermined materials and appliances. Or, you could do a combination of preconfigured with some customization.
It all boils down to what your constraints are... budgetary, timeframe, and subjective tastes. Lastly, once you make up your mind what you'd like to have built, you understand that it may not be possible to change your mind mid-way through the building process, for obvious reasons... Perhaps, changing the layout would require rewiring the plumbing and electricity, or maybe you run out of materials, or city permits would not allow the changes you wish to make, or maybe they would compromise the integrity of the construction, which would be unsafe, or maybe it would simply cost too much to make the changes you want.
The point is, that all of the factors that go into building a house are pretty similar when it comes to building a web site. The solution: coming up with a really good plan is a must. Finding a provider that will help you through the planning stages is crucial. Do not underestimate this stage of web design, because those who do usually wind up holding the shorter end of the stick.