My wife and I have been doing this for a number of years with no problems. When we enter Thailand I keep my wife’s US passport so if immigration asks, I have it. We just want to make sure that immigration does not accidentally stamp her into Thailand on her US passport. If that happens, she would only get a 30 day visa free entry and would have to deal with immigration as a US citizen for that entire visit.
they seem to go where the money is. A couple of years back they would not complete my 90 day report until I had fixed the issue. Brought my sister-in-law in, who’s name is on the house, and got the problem fixed with no fine. Still a bit of a hassle.
In the case of leaving the country, the issue is simple. Visit your immigration office within 24 hours of reentering Thailand. What often happens, is that when you leave the country your 90 day report date count begins once again, and when you show up for that next 90 day report, that is where they will see the problem and you could face a fine. If you are flying out of the country before the next 90 report is due, it is not a problem. This is only an issue with your local immigration office. The airports don’t care.