Why do I need to do a 90-day report if I am extending my ED visa every 2 months?

As mentioned they are two total different things. One is an Extension of Stay to be allowed to be inside Thailand. The other one is you report when you're 90 days inside Thailand. As you only get 60 days of Extension of Stay at the time, you need to make an extra visit when you are in Thailand 90 days. But you do not have to make this 90 day report on day 90, you can use the online system as mentioned from 15 days before till 7 days before due date, or by old fashioned mail 15 days before due date or in person or authorized person between 15 days before due date till 7 days after.

90 days online (but do it 20 days prior)

Those two are totally different things.

90 days report is specified by law that you need to report to the authority when you are staying 90days continuously (wording might be different).

Applying extension doesn't mean you are in country whole the time.

90days report can be done by online, or classic mail (via postal office) if you do it on correct timing.

You can try to search this group...

You only do a 90 day report if you have been in the country for 90 days. If you leave before the (89th) day the clock resets.

And you have to ensure your TM30 is in order too... .