Yes, you'll end up with the same as you would get on a store-bought system (but without extra guff that would usually be loaded on brand-name systems). As you note, you'll have the install disk rather than say a restore partition.
With a store bought system, the manufacturer/supplier would be supposed to help you if you had problems with the OS, eg if some drivers had conflicts or something. If you set up OEM Windows yourself, you'll have to work out any problems by yourself, since you have become the system builder. But of course there are folk here able and willing to help.
Edited by Platypus, 10 November 2009 - 06:45 PM.