If we had a custom build service (again), many things can go wrong, people are forgetting it is not just building a computer; it is everything that goes with it.
Yes, the items may be compatible to build together, however there are other things to consider. One example would be, cases, cases are fine to ship in their boxes to our customers, however when building a full system in the case the pressure and the weight within the system can cause a lot of carrier damage as some cases are just not designed for full systems to be shipped inside of them as strange as it sounds as they can be flexible.
Technical support, it is hard to give technical support as it is when something goes wrong as we have to know every specification, problems that can occur, errors, anything support related on the products we sell in order to have the items resolved, and when selling systems which we have not supported or configured before I could see the support taking much longer and would cause more problems which is not what we would want.
These are a couple of things which I could see could potentially be a problem from the top of my head and I am sure there will be more, however it is not my say if it should be in place or not. I know it was not hugely popular when it was on our website before, and it is easier to just call or email one of us if you are wanting a slight change to one of our builds which I have seen to be the most effective and efficient way.