Having the studs also makes it easier to locate the header clamps. Any Yamaha dealer should be able to order you one but Fowlers in Bristol hold good stocks of OEM parts.

Steel studs and steel nuts are not dissimilar metals so will not be subject to the galvanic reaction that would occur between aluminium and steel. However, should the nut stick to the stud then there's always the option of the stud undoing instead.

Like I said: "method in their madness"