@Alex ******
The first 90 day report must be done in person. Subsequent 90 day reports can be done online. If you leave the country and return, your next 90 day report must be in person.
The window to do a 90 day report is 15 days before your due date, until 7 days after your due date. Because the reporting window is so long, you are out absolutely nothing by trying to file it online 14 days early for the first time, or when you return from outside of Thailand. Maybe you'll get lucky and they will accept it, but officially they have to be in person. So if they reject it you still have plenty of time to go in person.