If you decide what is "there" in the text (or what you want "there" in the display), and you do this with explicit markup, I think you will be better off than leaving this decision, so crucial to your work, to the implicit workings of the TEI design principles. In you case, I would probably introduce <contents> on different levels - come to think of it, I might even use an attribute for this!
It helps me when thinking about this, that, as a matter of principle, elements can do all that attributes can so - and more. So faced with a problem like this (and being, frankly speaking, biased against attributes), I ask myself, which elements can help me bring about what I want?
> What if my source text is a modern printed volume with an editorial transcription and annotations? That is, the editorial work that I am encoding is a fundamental part of the text that I am encoding?  In the work that we've done in the publications department at the MHS, it helps to distinguish the transcriptions of the historical text from the contextual pieces that the editors have created to provide access to the text, but separating them out would be a misrepresentation of the source text that we used.
> won't know the best way to encode.
> standoff annotations indexed by xpath isn't a better solution.
>>>> containing interpretive data or metadata.
>>> idea of considerably lessening use of attributes would be cleaner.
>> then indexing and searching the original text would be much simpler.
>> The use of distinct namespaces would solve this problem.