It isn't uncommon.
On the back of the Precision Bass (at least my 1965 one) there are two filled holes in the body. One is a few inches from the neck pocket, the other closer to the bridge, both inline with the neck pocket. These are holes they used to hold the body during the routing process.
On the back of the headstock, mine has an extra strap pin. This was a tooling hole to hold the neck at that end.