Black "Appliance Epoxy" spraypaint is pretty good, Urethane POR-15 system is 10X better than the epoxy. Epoxy paint dries hard and can be chipped. Urethane base POR-15 stay a tad on the flexible side and won't chip. They made bowling balls out of urethane for a reason.
Neither can be applied to threads before assembly, as they will take up too much of the clearance and make assembly impossible.
Also, on thru bolts/rods, even though you can't paint the threads, make sure you paint the hidden part of the rod. I would do this even if I decided to use some sort of chemical finish instead of paint. I put my mortar together, then took out the black oxide coated through rods a year later when I was touching up the paint on the wooden base. Even though it was together only a year, there was a considerable amount of rust on the rods. It was thick enough that I had a hard time getting the rods out. I cleaned them up, painted them with epoxy spraypaint, and also sealed the inside of the holes in the wooden base with Spar Varnish.
Rick