It would depend on the company and how they run their business.
As stated, GM use a CNC machine of which they are a retail brand so they need to mass produce bats to go to these retailers. Other companies such as Salix are similar however they hand make their bats into their certain models - Both will take time selecting the right clefts for the right bats at a certain weight but different processes go into actually making the bats.
Custom companies run differently depending on how they run their business. There are some that make a bats to order, however there are businesses that have bats made into a certain shape and then they have a certain amount in stock to sell at a range of weights. Again, the clefts should be specifically chosen for a certain weight or grade of bat.
Overall each brand is different in how they run their processes. However every cleft should/will be weighed, planed down and hopefully check the moisture content before starting the bat - with the experience and skill these craftsmen have, they will have a good idea of the size of the bat that can be made from a certain cleft going on the natural weight of the cleft.