Brands do not matter. I am sure a small 'garage shop' builder can build an excellent frame as well.

Just make sure you get the dimensions you want. Some builders tend to push customers in their mentallity thus making you a custom bike you may hate. I see this happen.

Just tell them what you want and the tubeset you want and they will build. They may make tubeset recommendations according to their beliefs. So you need to be open minded.

All in all as long as you get the dimensions you want you will be happy.