With the global configuration like this:
pagination:
enabled: true
per_page: 5
title: ":title"
sort_reverse: true
and the page configured to paginate a collection through its front matter:
permalink: /updates/
pagination:
enabled: true
per_page: 10
collection: updates
I then build the navigation bar by iterating through site.pages, and I found that the page.url of the Updates website became /updates/index.html, even though the permalink should indicate otherwise:

Curiously, on pagination itself, paginator.first_page_path respects the permalink and the URL is /updates/, so this issue is isolated to site.pages.