@Jesper ******
read the original question.
It's about the FIRST extension. The 90 day stamp the Non O provided on entry has an expiry PRIOR to 90 days.
When you apply for and extension of that permission of stay immigration treats that as a report clock start.
From then on yes an exit and reentry (with reentry permit) the entry date starts the clock. BTW entry date counts as day one.
So you don't understand that then fine.
Google "does FIRST extension start the 90 day report clock AseanNow"
The visa forum discusses this often.
Check it out