yeah, that is the crux of it, isn't it?
Let me leave aside for now the stores that will sell branded computers off the shelf in configurations that you can then take or leave. I tend to frequent the other type of stores that work from components, the same way I would. (The branded configurations don't always consistently contain the same components, either, it seems.)
Now, the "component based computer stores" will also offer you ready-made configurations in their advertizing. But they will typically build one only when you order it. Fair enough.
What I find is that the "great deals" are usually configured to use up outdated components that need to be sold off. Last year's processors, hard drives that are a bit too small for me and memory modules that will use up all the slots to come up with an adequate figure (like four 256MB modules instead of one 1GB module, to give you an example of a few years back.)
Okay, such a machine, sold for a fair price and used in a context where more would be overkill is a good deal. But I tended to ask for the bigger drive and more memory in fewer modules (for the above example I might have asked for 2GB in one module.) By the time you are done with that you might as well have started from scratch, selecting a better motherboard to start with, etc.
So, nowadays I just do that. I don'T start from a cheap bundle and then replace most of it before I buy (still better that afterwards) but I ask myself what I want first and then start configuring. Yes, with upgrades in mind (within reason.)
Upgrades: We are mostly still working with a technology that is highly modular - your next hard drive or optical drive will easily replace the old one or run alongside it. But when it comes to memory and processors the story is a bit disappointing. When the faster processor you always wanted becomes cheap enough you will probably discover that it isn't THAT much faster anyway - in your system. And the old memory that your motherboard will hold has not come down in price as much as the new modules being advertized - in fact it is now exotic and will probably cost more than it did back when you first bought that machine.
So I replace mobo, CPU (with fan) and memory as one unit, most of the time. And I see that as essentially "a new machine."
But you don't always need the latest greatest specs, either. The machine that I am typing this on is running with the once incredible amount of 1GB of Rambus (!) memory (Don't be afraid, go ahead, google it!) AND its mainboard IDE interface cannot support drives > 128GB. I have bigger systems - I need them - but this one somehow survived.