I use Si Racha immigration as its closer to my home than Jomtien. I believe your supposed to use your closest immigration office. Unsure where in Chonburi you are but if your in Pattaya I would expect you need to stick with Jomtien. Never been there but I hear its a pain.
He will have no issues as he is not entering Thailand every month. I was also on a
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rotation and used the visa exemption for many years. Immigration then stopped me on one occasion and told me to get the correct visa as I was not a tourist. I did as asked and got an extension to stay as I was married to a Thai.