That's because they use parts that are inferior to what you'd use if you built it yourself. That is NOT a benefit.
I just built a mid-grade gaming PC. Skylake i5-6500, ASUS H170 PRO gaming motherboard, 8 GB RAM, 250 GB SSD, 1 TB WD Blue Hard drive, Antec 650W 80+ gold PS, Bluray burner and a Radeon 7970 with 3 GB.
I built it for $741.
How did I do it? I went on pcpartpicker, researched and made a list of the parts I wanted. I availed myself of the 25% off at jet.com and scoured buildapcsales on reddit. I even scoped out new parts on Ebay. In the end, I did not settle at all. I got all the parts I wanted for much cheaper than it would cost to buy a pre-built system with those specs.