The deal of designing your own system is getting to choose and design all the parts you want in your new rig. You can choose the brand and model of the motherboard, CPU, RAM, SSD, Hard Drive, optical drive, case, power supply...
It is not so much to save money but the ability to choose the best qualify parts for your build.
When you buy a prefab system generally the manufacturer makes compromises to reach a price point or get rid of old inventory. A brand of the RAM or SSD or other component may not be listed, so they can sub the cheapest parts in at the time of your order. I've bought one prefab unit a 286 model and it was a pain. They motherboard manual didn't match the motherboard so to add RAM I had to call the manufacturer and wait on hold for hours to get a tech to get the right setting on the motherboard it was a nightmare. So for me after that one experience I've built all my own rigs ever since. I'm not saying all prefabs are bad or junk, I just like to know exactly what is in my rig.