Congrats on his visa approval. Tourist Visa details have not been changed. It's still 60 days stay on entry. Valid from/until, visa validity, is the term you can "use" that visa, not the length of your stay. That means during those 3 months, you can enter on that Tourist Visa to get a 60-day entry stamp.
You need to check the reason for rejection in that email notification.
It could be because your current stamp expires BEFORE your 90th day. The 90-day report is for reporting that you are legally staying in Thailand continuously for 90 days. With the current stamp, technically you will be overstaying on your 90th day.
Anyway, you are supposed to go to the local office on 5th October to get the 1-year stamp. You can submit a 90-day report in person at that time.