My ex wife managed to fight her way into there and stop me from flying. Just saying but yes get the document from Amphur it is a special paper for permission to leave the country.
You can go to the Amphur and get a document for that reason. Otherwise yes could have an issue. She can not get in to immigration with you but she can wait outside and if called for they can bring her in. But get the paper from amphur and you god to go.
Yes you need to and yes unless you leave the country before 90 days you need to do 90 days reporting. If you leave the country you do not need to do a 90 days but then you need to do another TM30