yes i have put 5/8-18 threads on jackshaft ends and use 5/8 nut. but it's not the preferred method in my eye. i like center drilling and tap 5/16-24 and use a bolt/washer instead. Though i like the large nut on the end of the jackshaft (that's how rupp does it for example), the 5/16 bolt has less protrusion at the end of the jackshaft. and therefore less crap to rub on my foot! on Rupps this is not an issue, and the 5/8 nut is fine, as the torque converter cover hides the nut. but on speedways for example it's a huge deal, and the 5/16 bolt is better.
as for the 'crush' idea, if the jackshaft is the right length, this is a non-issue. also with the 5/8 nut, most people over-tighten the nut, and screw up the whole system. also if the nut is rubbing on your foot, it can come loose (even though it is a nylon lock nut style.) And tear up your shoe! i just don't like the nut idea if the end of the jackshaft is exposed.
if you really want the 'crush' idea on a jackshaft that is drilled for a 5/16" bolt, you can use a 5/8 diameter washer on the end of the jackshaft on one side. personally i just make sure the jackshaft is the right length, but you can do it that way too if the jackshaft is a bit too long, and you don't want to dial in the jackshaft length.
but the one thing i'm sure we can all agree on, the roll-pin idea on a jackshaft is no good...