I think Bruce gets the points on this one. Those photos look like they show a single larger hole for an index pin.
Well, I actually do this professionally. I design processes, tooling and fixtures for....routing bass bodies. For CNC machines and old-school non-CNC Pin Routers. Holes and index pins are the common method of aligning parts in machines.
If you are curious about this stuff, check out my long thread about Pin Routers. In there, I show how I use steel dowel pins to index blank parts onto fixtures.
https://www.talkbass.com/threads/pin-routers-the-old-school-production-workhorses.1405214/
Like SteveCS points out, we usually use two index pins to accurately line up the part. There's commonly a second mysterious hole back under the bridge. Those two holes are a clear sign of a CNC-cut body. They are usually about 1/2" diameter x 1/4" deep.
The reason for that is that they are cut with the same router bit (usually 3/8" dia) that cuts the neck pocket and pickup cavities. After the bit has finished routing out the neck pocket, the computer code tells it to move to the center of the neck pocket, plunge down 1/4", and spin a little 1/16" radius circle. The result is a 1/2" dia x 1/4" deep shallow hole, accurately placed in relation to the other features of the body.
In the next operation, the body blank is flipped over and placed into another fixture. That fixture has two 1/2" dia x 1/4" high steel pins sticking up. The body blank pops onto those two pins to line it up accurately. Some other clamps are secured. And the operator presses the Go button to start the next sequence of routing operations.
That's probably way more technical info than you wanted, but that's what those holes are for.