Encumbrance over a mortgaged property
After the mortgage registration the owner (who is called the mortgagor) cannot create any encumbrance on the land without the consent of the mortgagee (the lender in a mortgage, typically a bank). However, with the consent of the mortgagee (say when it is a private loan from you to a Thai national) the land owner may lease out or give a right of usufruct to another person (even to the mortgagee) but you should include this option in the mortgage agreement registered with the land office, with the consent of the mortgagee the owner/ mortgagor (the borrower in a mortgage) would be able to create an encumbrance over the mortgaged property land, even for the benefit of the mortgagee.
The downloadable mortgage contains this option.
The issue of the Thai national being your agent or nominee
It is not likely that the land office (unless you do it all within a short period of time) will raise the issue of the Thai national being your nominee owner because this should have been raised upon registration of ownership of the property. This already lies behind you and you could try to register a lease or usufruct (no guarantee). I would recommend to use a Thai lawyer with connections at the land office and expect to pay a few thousand baht 'extra money'.