You're right. The MkIIa does have a flat on the shaft for just the reason you suggest. I'm not sure whether later MkIIs have it as well though. I got mine in October 2000 and mine doesn't have the flat. This is something I'll have to keep in mind if my custom Fascias, Buttons & Knobs ever get into production.
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Marcus 32 gig MKII (various colours) & 30gig MKIIa