It looks kinda like they had to remove that part in order to give clearance to the clutch components right there...
The funny thing is that there is a pic around here somewhere, I think in the thread about changing out the cam chain, where the cam shaft looks like it had a chunk missing too. What kind of manufacturing practices are they using? Instead of a a machine, we're going to use TNT to remove that little piece...

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As long as it rides good, I don't care