Seems a backwards question. I would think there are things a customer needs to ask a competent gunsmith. Mostly those things won't be known to ask until a person actually has need of a custom rifle. The reason to get a custom would be to change those things that you ask the smith about,from what you could get in a production rifle.
RH you are correct...almost. You should have a good idea about the type, components to be used and purpose of rifle you want to build but listen to suggestions the gunsmith may give you about the finer points of the build. You should be asking questions and he should be asking you questions. If you find that he only wants to do things his way, you may need a different gunsmith. Don't go to a smith who builds 'tacticool' rifles and expect him to be able to rebuild a mauser 98 with a beautiful English walnut stock, it ain't gonna be pretty. Find a smith who builds as close to the type of rifle you want and try working with them.
Its like buying anything else, the more research you do the more informed you will be and be able to make better decisions. WRITE the specifications for the build, do not trust that they will remember what you agreed upon.