If you are looking for certain specific specs then it might be cheaper to build your own, but typical CTO computers are much cheaper.
A big benefit of pre-built is the warranty, and tech support from the manufacturer.
If you just buy the components, they likely will all be under warranty, but likely won't be as easy to deal with.
Keep in mind that the cost of a legit OS isn't that cheap if you buy the license.
I would suggest to get a pre-built and upgrade yourself the RAM, add a SSD, and the graphics card.