I believe it's a different "work permit" system for Burmese, Loa, Cambodian etc. Not the same as us Falang. Also due to the ongoing issues in Myanmar there is a back log for passports and such so there is actually an "amnesty" in place, but he should be up to speed with this I would have thought.
The accountant/ lawyer who helped you to set your company up will be able to assist. You don't want to VAT register until you hit the 1.8 M THB annual income mark