Hi Chris,
There are couple of better approaches to adding default “stuff” to a document.
First, you can create template files. These are what you see when you run the New command. Template files can hold pretty much anything you want (layers, linetypes, layouts, geometry, etc.). To create a Template file, just save your document to the Templates folder.
For materials specifically, a better approach is to make sure the materials you like and use frequently are part of your material library, which is external to Rhino. This way, your materials can be quickly dragged into your current document. The advantage of this is that you can share your materials with your colleagues, plus you don’t pollute your documents with stuff that you aren’t using. To see what’s available in your material library, click Panels → Libraries.
Yes, this is expected. If you don’t want every object to have a material, then assign materials “by layer” instead of “by object.”
Hope this helps.
– Dale