A home-built system you are responsible for supporting, or at least dealing with the different warranties for the parts, you also need to purchase the operating system, put it all together, install drivers, etc...
The biggest advantage to an off the shelf system is that you just buy it and turn it on to use it. You also have a single point of contact if something breaks.
The cost vs you buying the same parts is for the support and cost to put it together. With some builds you can actually get it cheaper from an OEM since they buy in huge quantities and can get discounts on parts. Low end systems you may be better of just bying stock, mid and gaming systems, building your own is best.