Very nice summary from Tradesman1, as usual. In answer to your question about whether the performance/quality difference is worth the extra money, that requires a value judgement on your part. The vast majority of PC users wouldn't know the difference between good DRAM and bad DRAM, and couldn't care less. There's a small segment of society (many of whom populate this website) that does know the difference and care greatly. It's like the difference between someone who will shell out money to add an aftermarket exhaust or air-intake to their vehicle in order to get more horsepower and/or better gas mileage, compared to folks who only have a vague idea of what kind of MPG or horsepower their car gets in the first place. If you fall into the first category, then yes it's worth it. If you're in the second, then no it's not.
Anyway, on to the purchase comparison I mentioned earlier. I'll use the Sager build as an example since I'm more familiar with them:
Having recently purchased a Sager build, I know that the stock memory that I got was Samsung M471B1G73QH0-YK0. I just got the model off the stick itself, but I also found that info online and was expecting it when I purchased it. I have no way of knowing whether every custom build with stock SDRAM will come with the same, but being pretty familiar with the economics of component stocking, I feel safe assuming that Sager got a good deal on them with a bulk purchase and will ship them until that lot is depleted. That being said, here are your options:
Option 1: 16GB stock SDRAM at 1600MHz - 2 X 8GB [+$90.00]
Option 2: 8GB stock SDRAM at 1600MHz - 1 X 8GB [+$0], then add a matching stick for @ $116 on eBay or $147 at Memory4Less. [+$116]
Option 3: 16GB Kingston HyperX CL9 at 1600MHz - 2 X 8GB [+$160.00]
Option 4: 8GB stock SDRAM at 1600MHz - 1 X 8GB [+$0], then replace with 16GB G.SKILL Ripjaws Series at 1600MHz - 2 x 8GB for $155 at Newegg [+$155]
For the stock SDRAM (Options 1 & 2), it's obvious that it'll be cheaper to get it with the build rather than trying to add in a matching stick later. The main reason for this is that particular SKU is not commonly available, since it's normally sold as an OEM part under contract rather than retail. The major drawbacks to this option is that, aside from being CAS 11, the lot was probably not binned for quality beyond basic specs (see Tradesman1's post), and the two sticks will be tested together prior to shipping your laptop, but they will not have been binned together as a matched set.
For the name-brand SDRAM (Options 3 & 4), for such a slight difference in price, it would seem easier to just get the Kingstons with the build for only $5 more. If you go with Option 4 however, in addition to saving $5 you'll get a set of sticks that were binned, tested and matched together. There's no way to know if the same is true of the Kingstons. Again, they'll be tested prior to shipping, but that's pretty much all you can take for granted. An additional benefit to Opt 4 is that you'll also get the 8GB stick of stock SDRAM. You can sell it, use it to upgrade another laptop, or try it out with the two Ripjaws - if they play well together, the set won't be as fast as the Ripjaws alone but you'll have 24GB of usable SDRAM.
Note 1 - This comparison process works for other components as well, like the SSDs, HDDs, etc.
Note 2 - I currently own two Sager gaming laptops and love them, but if you decide to buy a Sager I highly recommend you buy it through xoticpc.com rather than direct. You get the same or more build options, the component prices are the same as Sagers, and xoticpc has great customer service. If you need to RMA, repair, send in for upgrade, etc, they'll deal with Sager for you which is huge because Sager customer support sucks.
Note 3 - Make sure that if you're going to do upgrades yourself, the system you get allows it. I could be wrong, but I believe simply removing the back cover voids MSI's warranty. Someone can correct me if I'm wrong.