At the moment it is known that the Thai Elite Visa and the Thai Consulate in Penang Malaysia looking for overstays in the past en may refuse applications.
What others will do in the future is what we will learn in the future, advice is to always avoid to go on overstay as there are options enough to get a legal stay.
You need to report that you are 90 days inside the country, even when you leave after 104 days in the country. You will not get fined when you leave the country, you may get fined when you are back in Thailand and try to make a new report if you stay then 90 days or longer.
BTW You also need to cancel your Extension of Stay at the same Immigration Office where you got the stamp, it does not cancel itself or by eaving the country.