What happens at the store is this:
A laptop is put on a shelf with a placard that tells you it has an Intel Processor ... knowing that most store customers will walk in see Intel and say "Oh that's good, I heard of Intel, then it will say GFX card and xx GB of memory... and usually that's about it ... in order to make the price attractive and have the highest profit margin, the rest of the components will be low budget options, that ... if ya had the choice, you would have invested $5 - $15 in upgrading many of them.
With a custom build, you get a bare bones machine, then you decide:
a) Do I wanna spend $XX for a better processor ?
b) Do I want the 970M or spend an extra $xx for the 980M ?
c) Do I want that slow 5400 rpm HD or do I want a fast 7200 rpm unit ?
d) Do I want the base 8 GB or 16 GB for $xx
e) Do I want the ow budget WiFi or spend $5 for the good Intel one ?
f) Do I want an OS installed or not ?
g) Do I want normal delivery or spend $xx for it to come faster ?
That's pretty much it. Tho if you are going to buy a store bought unit, MSI is the ONLY one on the shelves that was made by the company whose name is on the box.