I would mask it with a neatly cut bit of tape, then when you flat the bay down go over that area with a thin coat of normal primer and colour, some cars have the VIN in primer from new,
If you are using something like Lechler, I would suggest only putting one coat of epoxy over the VIN followed by colour. Provided your coats are not too heavy that should be fine. Mask it if you need to do additional coats generally. Unless you are trying to do a really swanky paint job in he engine pay you may find one coat of each sufficient.
For that area you can see that lip above and below. I could do everything below first and the rest of the engine bay for 1 coat and second coat include that area