G'day Sunbeam,
I don't think Bill meant leaving the STUDS loose, they have to be screwed home into the rocker box before fitting. I'd say he meant the 5 bolts.
I'd say the longer studs were fitted to use external nuts instead of the sleeve nuts. It would be impossible to fit the box on with them fitted to the box with the motor in the frame. Would have to drop the stud into the head, loose fit the box, screw in stud, finish fit box then put the nuts on. Would be a nightmare to get off.
Cheers