Making a skip bolt some call it a shoulder bolt

[Frank S]

I guess I'm confused by your shoulder bolt, it seems your more making a sturdy threaded extension of the trolley truck pivot so that the hole does not elongate or rotate from the perpendicular mounting you want. I guess in my narrow view a shoulder bolt is used as a pivot axis for some other part in a machine.

I've made shoulder bolts via a fourth way (sorta your first method starting with raw hex stock), start with the next bolt size larger, machine the threads off, and any shank of unthreaded down to the hex head of the shoulder diameter you want, then machine the length of the OD for thread pitch you need, leaving the desired shoulder length, single point it or use a thread die.

I typically will support the bolt with the tail stock and a center drilled into the end of the bolt.

It should be interesting to see what your making with all these jigs and fixture posts of late.

The trolley truck allowed to pivot on the shoulder of the bolt, since after the bolt is tightened into the locating hole the truck still has a few thou. clearance.
The reason for the step nut being welded in place it to provide a land or a stop if you will to provide a positive locking location for the bolt this pilots the shoulder as well placing the threads of the bolt in tension and not shear. There is no possible way for movement other than rocking pivoting motion on behalf of the trolley truck