During an update, the new app is written out first. User data files that need to persist are then copied from old /Documents to new /Documents, and then the old app is deleted. Everything else in the app structure is new.
This line from that doc on Library/ illustrates: Your app should not use these directories for user data files. So, yes, old Library/ on the device is deleted during an update.
Whether or not the new structure mimics the old at that point is basically up to the dev, based on.
thanks for your explanations that remove any doubt I had.