I work in the Architectural industry. The process of design and construction is a partnership between owner, designer and builder. The role of the architect is to place into the construction documents enough information to define the design, provide performance and material specs and to determine constraints. The role of the contractor has been to develop the means and methods and to construct the project in accordance with the performance requirements given in these documents. The role of the owner is to define the building use and provide financial funding and constraints.
So I look at CAD Standards as a relationship similar to the one above. The CAD Standard defines the goal, defines the end product and determines constraints. The CAD User defines the methods and means for achieving that goal, works toward a consistent end product and lives within the constraints. I do not think you allow users to run wild and create files any way they please. But I think the Standard should not be the place to define “how” they create files.
You may want to develop a secondary document that supplements the standard and leave the how to methods out. This would allow you to give your standard to the client without giving away your superuser CAD methods.
The CAD Standard may at times define methods when it impacts production speed or where a number of legitimate, but differing “paths” to get there. When the methods need to be unified, the Standard should speak up. When the methods don’t matter, then it should remain silent.
I believe the CAD Standard you develop should be a target to hit and not a path to follow. It should be goal to achieve but not the step on how to get there. Delve into the steps only when those steps help unify the production methods and the way the files are constructed.