These are effectively per-document preferences that can, if desired, alter the defaults for some System attributes. The Document Settings dialog tabs do not list attributes directly, but rather some of the controls have the effect of altering the built-in default values of some of the System attributes (c.20 in all).
For instance, the font used for all note text is 'MercurySSm-Book', a serif font. But, you may prefer a non-serif such as 'Helvetica Neue'. By changing the Documents Settings ▸ Text tab's ▸ Text Font control to 'Helvetica Neue' you are in fact seeding a new default for the system attribute $TextFont—but only for the current document—which tells Tinderbox which font to use when adding text to a new note.
System attributes whose defaults by Document Settings cannot be edited in the Document Inspector's System tab—use the appropriate control in Document Settings.
Next in the cascade are Document system attribute defaults…
See also—notes linking to here: