Well bolt holes are not the best method to control the block in all 3 axis. Bot hole are typically 1/32 over sized for 1/4" bolts so they are to small for 5/16 bolts and allow to much rotation because of the oversized hole wit 1/4" bolt.
When I build my rim my mold is pinned to a 24" x 20" sheet of 3/4" MDF this has a centerline scribed and a neck block guide blocks that fits the width of my neck block and maintains the block in vertical plane squareness to the center line and allows me to press via a turnbuckle as screw press, the block into the side material and thus both into the wall of the mold. This insures the block is both square to the centerline and the the side with zero though given to it. Once the blocks and sides are glued up I no longer use this piece of MDF.
Original design sketch
Attachment:
neck bock fixture.png
Attachment:
neck bock fixture close1.png
Besides you would have to cut some sort of bolt access in to the sides at the location of the bolt holes and this is on the center line of the joint prior to glue up so you would be providing a point for possible crack to start