You could indeed enter thailand on a new eVisa even if you have an extension/re-entry permit in your passport.
Just make sure you have the eVisa PDF printed out, and make sure the officer knows you don't want to enter on your currently valid re-entry permit tied to the earlier stamp
You APPLY to file a 90 day report online and as soon as you submit the application it sends you an email with a partially filled out TM47 <- application for 90 day report that is headered like this
This means it was not approved and they'll usually have a reason in the email as to why
So in your case you just wait it out and see if it's approved or rejected. .
Remember though just because you applied to file a report online, if it's not approved or rejected before the due date you still have to GO and file one within 7 days after the due date or you will get a 2000baht fine for late filing.
the person who told me travels so much sometimes he's in/out of the country 3 or 4 times in one 90 day period, so he's only done it once or twice where he's been here long enough to file 2 reports
Remember your first 90 day report is due 89 days from the date you stamp in to the country and you can do a 90 day report up to 7 days after the due date without a fine
I know someone on a DTV who does his FIRST 90 day report after coming back into the country on the 95th day (6 days late) and that means they don't have to do the second one because the 180 day entry stamp will run out before the due date of the next report
He's had a DTV since the program rolled out (July 2024) and only ever done ONE 90 day report before he exits/re-enters the country to get a new 180 day stamp
you can file a TDAC in the arrival hall of the airport before you go to stamp in. At Don Mueang and Suvarnabhumi they have kiosks (dunno about the other international airports)