UIBuilder Questions

• Yes, the UI Builder will learn to deal with multiple (or zero) USS files per UXML. This will enable you to share USS files across many UXML files, as you can already do when writing UXML manually. But also yes, this is not currently possible when just using the UI Builder.
• It should be possible to parent elements under UXML template instances (I assume that's what you mean by UIDocument?), but only at the end. But this is not really encouraged in general. Even for default Unity controls, like IntegerField, it doesn't make much sense to parent elements inside the IntegerField. Some elements do actively support this, like Foldout, where they define a special inner element to act as the "container" for all children.
  In either case, the insides are grayed out because the entire subtree is an instance of another UXML document (or custom C# element) so it's not editable. You have to open for editing that UXML document if you want to change the internal hierarchy. We have plans to make this switch easier and more in context in the future.

 

There is a specific feature in UXML for overriding attributes of elements inside a UXML template from the main UXML doc. This uses <AttributeOverrides> tag. This feature is not yet supported in the UI Builder but should be eventually.

However, styles can easily be overriden. You should be able to inspect elements inside a UXML template instance in the UI Builder and find out what style classes they have. Using these classes (and names if necessary), you can create USS selectors that match these classes and override the styles of elements inside the template instance.