Program Updates in Microsoft 365 for Education

However, if I'm reading this all correctly, the ~20GB per user does not account for additional storage used by things like SharePoint Sites that can have quotas up to 25TB. So am I to understand that 4 maxed out SharePoint sites will use all 100TB of our base storage for all users/OneDrive/SharePoint?

Correct. Guidance will tell you to set quotas for SharePoint sites as well, but the only documented methods I'm seeing is to set per-site quotas. (i.e., no "default" site quota) If you're a large org that allows M365 Group creation for end users (ahem.. which Microsoft also heavily suggested to higher ed orgs), the current solution I see would be a daily PowerShell script to cycle through all sites and force quotas down to whatever you wish. At least this is what we'd have to do, since there's liable to be any number of new M365 Groups created through Teams/Outlook/etc on a given day with over >20k users. Orgs that don't allow users to create M365 Groups or SharePoint sites will have it much easier on this front.