As a quick and dirty response off the top of my head, it would seem to me that there are two points of focus for two parts of your projects.
For the SharePoint (SP) structures the focus probably would be best on each structural design -- a sort of "This is what it is supposed to look like" approach. It will probably be difficult to go any deeper than that at the beginning. If someone sees a need to "control" at a deeper level of detail, you can concentrate on what it would take to control the more detailed item. Of course, the whole thing is driven by the business requirements of each individual SP site.
The UI consistency issue can be controlled by comparison of the designs. To use your example, if the requirement says add a list, then the proposed change document would be updated to indicate all affected SP product designs. During audit or review of the products, you can compare the affected SP designs for "sameness" and compare each product against its applicable design.
Regarding the Custom Code, may I assume that there is a set of one or more scripts for each SP project? If so, then each set will be a component of its respective SP project.
I hope that addresses the question and helps or gives you some ideas.
