In general the re entry is near but separated from passport control. Pasportcontrol is just looking at your papers and stamp your paspoort. Re entry is some more work! Photo and paperwork. So i expect near each other but reentry first .
As far a i know if you have ltr you do not have to file 90 days! I have one and never do that. Only one time every year but if you are not a year in Thailand you do not have to do that!