I think it's still cheaper to build your own. What makes it more expensive, is when people want top quality in their systems, and those small but insignificant(performance-wise) parts add up fast. Like buying the board with better capacitors and 2 extra USB slots, or a PSU with better efficiency and power ratings, versus the one that comes with a prebuild that is slightly more sufficient than minimum. Multiply that by all the components possible, and there is a difference.
Especially when you consider that a good board can eek out a 1% boost in performance for the CPU, and then another 1% for the ram, 1% GPU, 10% storage. Then you buy better than average CPU, GPU, Storage, and those models put out a slightly better performance and efficiency number than the same components found in its equivilant prebuild. You end up with a system that costs maybe 10% more to build for numeric part for part, but the performance is also closer to 15% quicker. So between the gratification of knowing how to build the system, you also bare the fruits.
But that's just my own .02. My system is silent and temps are never above 30c at load. So for me, its an art form. Not bad for a dual 12core system.
At least with the cheap parts from whatever manufacturer, you'll feel better because of the support and warranty that is there for the whole system as a whole. Where if you build the system, you have to deal with taking it apart and sending in the faulty component.
Last year I had to RMA 1 item, and I have just as much luck with prebuilds of any brand as I do home builds. That's just the nature of the business. Sometimes you want to just let them take care of it, and sometimes your annoyed that you can't just send back the bad part.