There is a 3rd alternative, get the spokes unthreaded and long, thread them yourself and trim to length once installed. Had to do that more than once on bicycles AND motorcycles... especially on a custom/retro bike (and yeah, I'm a sucker for the XS650, nice job so far) sometimes the only real answer is to do it yourself and do it right. PITA? You betcha. But the results are worth it.
Please tell us how you 'unthread', I'm sure we'd all like to know that!
Aftermarket spokes and ******* are often a roll of the dice. That said, I'd just remove the spokes and grind/file/sand them down. I'll also note that some spokes have threads that are rolled on rather than cut. This means that you can't always cut the threads unless you're given a dead on diameter of the spoke at the '******' end as a reference. And I, as former MC dealership mechanic, can tell you that spoke hassles, both OEM and aftermarket, are par for the course. Seen some serious 'near coming to blows' arguments over spokes, *******, and lace patterns (patterns being very rare tho).
Meanwhile, I'm a big fan of XS650 twins.
Aftermarket spokes are not often a roll of the dice. I've been spoking since 1968 , always using aftermarket spokes, never come across this problem before. There are such things spoke length calculators and mathematical formulas to work out spoke lengths. Before the advent of the internet you got you spoking info from books. For this you input rim size, hub size, spoke number and cross pattern. Spoke thread length is standard across the board to accord with ****** length. All ******* have a thread free section at the beginning of the ****** to account for discrepancies caused by various things. Honda, Kawasaki, Yamaha, Suzuki, Harley, Triumph, Ducati, et Al, do not make their own spokes, they use spokes from various spoke manufacturers, so in effect there is no such thing as OEM spokes. The same is true of many items that go into the manufacture of all cars and motorcycle, and even bicycles. Of course manufacturers carry spares for their vehicles, so while you may well order parts from the parent manufacturer, that does not necessarily mean the manufacturer actually makes these parts, they may stamp panels, cast engine blocks and manufacture many associated parts, but not all as it is not economically viable. Many parts are manufactured by an external manufacturer to the parent manufacturers standards and sizes. Examples: Seat belts, bulbs, cables, bolts and nuts, wheels, tyres, filters, hose, paint, springs, exhausts, mufflers, and yes, even spokes. this list is not comprehensive and not true of all manufacturers. The same is true of manufacturers of pretty well everything: TVs, houses, fridges, washing machines, furniture and so on. Manufacturers typically go the cheapest route!