Thai Immigration has recently started to send email reminder notifications that a 90-day report is about to be due.  It seems they send around 15 days before the due date, based on the date of the last online report.  I just received a notification.  But it does not take into account the "clock reset" that should have occurred because of a recent trip out of, then back into the country.  Can I safely ignore the notification and only do the 90-day report I think is due 90 days after my recent last entry?

Yes. That is exactly what I did in August last year, made the correct 90d report in October without any issues, received a new 90d warning for the October report end of December 

Same for me. You can ignore it. The system is not connected to the border checkpoints.

Report is due on day 90 from your last entry.