You're probably right about their motives.
However...
[3] was at the heart of my assumptions. You're right - the phone had not updated its backups prior to the password reset.
Why? We don't know. There are several possible reasons, but we don't know which one is the right reason. That means that there is a chance that a new backup could be triggered, under the right circumstances.
What we DO know is that the password for the cloud and the password on the phone are now out of sync.
If there was a way to get them back in sync - i.e. find a backup of the account details and restore it - the phone MIGHT perform another backup to the cloud. Apple can almost certainly tell when the latest backup occurred, so they will be able to tell if the phone does another one, after the old password has been restored to the cloud.. Change the password again, and you've got the latest data.
As far as the "backup of a backup" question goes, I'm not convinced that holds true. The actual data/files/etc backed up to the cloud - yes, I can see that argument to an extent.
The account settings, on the other hand, are far more important. In a hypothetical case where Apple were hacked and a lot of customers accounts deleted, I can't see them wanting to be in a position whereby they had to get all those customers to contact them and re-verify their identities. If there are no backups of that data, then they're not the company they appear to be.
I would be very surprised if A) they didn't treat device contents and account data separately, and B) they had no backups of the account data. But, I suppose, anything's possible.