Is the first 90-day report due 89 days after entering Thailand or 89 days after receiving the non-O retirement visa?

They have not made a mistake. Until you received your non-O visa/extension, you were not on a stay that could exceed 90 days so you were not subject to 90 day reporting. But once you got on a stay that could exceed 90 days, the counter starts from that day. The paper your received from immigration is when your first 90 day report is due.

No. They've got it right. You go by the slip of paper they've given you