Just being paranoid here, sorry for a dumb question of sorts.
The ANALYZE run post upgrade, that doesn't include having to run it on the postgres database, does it?
It is only for the databases that you manually created for your application?
The postgres database is soooo tiny, an after-pg_upgrade ANALYZE of that table would take seconds at most, unless you unwisely put user tables in the database? IOW, don't worry whether or not it gets initially analyzed.