that part says "this license document" and that refers to the very text in the document that is claimed to be the AGPLv3.
It does not mean it is not allowed to license a work under another license that makes references to the AGPLv3 and includes it, only that the included document should not be changed.
This doesn't preclude additional restrictions (or permissions) in a supplemental license file. Section 7 practically encourages augmenting the license.
Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.
Above requirements include:
All other non-permissive additional terms are considered "further restrictions" within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.
