This also happened to me before. So when I returned the day after my permission to stay expired , in accordance with immigration instructions, they still did not have my passport back to give to me ( it was for a marriage 1 year extension and they had to send it out of province for the approval). They said come back in yet another week to get my passport back and told me not to worry re an overstay. When I returned in a week they had my passport with the one year permission to stay marriage extension approved. .. Still I was uneasy for the entire week with no passport and knowing my old permission to stay had expired. But they told me not to worry. What can I say other than this is Thailand.
The most difficult process for him may be to open a Thai Bank account when on Visa exempt status. I was able to open a Thai bank account 6 years when Visa exempt but I have read this is much more difficult to day than it was 6 years ago. I recommend he attempt to open an account ASAP after he arrives in Thailand.