Find a new gunshop! The guy your talking too, doesn't know what he is talking about and who knows how far this lack of knowledge will go.
The parts sold individually are the exact same parts that they build the complete rifle out of, which is true of most (if not all) vendors. If what he said was true, then if you bought a complete rifle and the a spring broke, you'd have to call the vendor and they would have to replace it with the spring from the 'good' pile.
The reason you save by building yourself is because you don't pay the 11% (or somewhere around there) Federal Exice Tax on completed firearms.
You do lose the warrantly on the complete rifle, but not on the parts. Although this is also depended upon the manufacturer. Some will service a home built as if it were built in their factory, as long as all the parts are from them and it was properly assembled and not modified.