Dear Miss Snark,
If there was something bizarre about the format of a novel (think "Pale Fire"), would you want to know about it in the query letter?
No, and yes
The purpose of a query letter and accompanying five pages is to show me you can write and persuade me I want to read more. You'll need to tell me about your weird formats, time shifts, loathing of the vowel e, and other sundry mattrs (ha!) in the cover letter to the partial.
You don't need to tell me anything except what applies to the pages I'm reading.
The yes part however is that a short description of structure, particularly if it's Pale Fire, is ok.
The problem here is of course, hardly any of you are writing Pale Fire, and thus will waste paragraphs telling me about alternating POV that starts on page 20 or voyages back in time that start on page 30. Or both, which start on page 40.
There's a difference between structure and what happens in a book and devices to develop plot. I do want to know about structure; I mostly don't want to know the other.