I think it really depends on the the options. Some options lead to steps that a normal build does not experience. For example if you choose an Adirondack top there are some extra steps that go into the selection, and cutting of the top that a standard Taylor does not go through. Same for selecting a short-scale neck on a non GC model. For short scale to work on a non GC body the build setup for the top has to change. The bridge is in a different location which leads to positional changes in the bracing. Because so few guitars are selected with these options more attention has to be paid to how it is setup, otherwise the guitar may not meet Taylors QC standards which are high.
On the other hand if your choices are simply aesthetic such as back and side choice, inlay, etc then you are just plugging in different pieces into the normal assembly line production.
In either case the individual selection of woods and final steps are more rigorous for BTO (which I believe is not called custom again).