Here's my 1981 VSB-80CSR. A-stamp on the neck and in the body and definitely nitro finish.
A for nitro seems like a good theory to me. Any deviation from standard poly finish (nitro, cashew or matching headstock) would need to be passed on to the paint shop, and marking the part itself seems like a good way of doing it.
The placement of these V and Y marks in bold magic marker in the neck pocket during the mid 80s makes me wonder if it relates to the necks fitting to the bodies?
Note how this Y is stamped in the body code and additionally written very clearly in the neck pocket.