KZ550 Set Pin Length

Hiya Guys.I've got a bit of a puzzle here and would be very grateful for your input.
I'm rebuilding a 550 engine (1980 A1) and have fitted new crankshaft shell bearings,seals,primary chain,and cam chain.
At the moment I have the upper crankcase upside down with the crankshaft fitted in place.
I'm at the point where my next move is to fit the drive shaft and output shaft into place.
The factory manual specifies that the "set pins"must be fitted before the drive shaft and output shaft are fitted.
The set pins are meant to locate a hole in the outer bearing race on the end of each of the shafts.(Presumeably to stop the outer race from spinning when the engine is running.)
The problem I have is that I measure the set pins to confirm that they are the correct parts and they are.
But they are 16mm long.(which is correct according to the factory manual and the exploded diagram on Kawasaki.com).
I then measure the depth of the holes in the upper crankcase and find they are 17mm deep.
This means that the pin can sit 1mm below the surface of the crankcase,therefore doing nothing usefull and failing to prevent any spinning as previously mentioned.
Hopefully the pictures I took with the phone camera will show up below.
Bit of a puzzle so any comments and/or input would be very welcome because I can't progress until this is worked out.

Someone correct me if I am wrong but I seem to recall that these pins are a snug fit and have to be gently driven in. They could be driven in part of the way if it is a tight fit, but the yellow flag is being thrown in my mind even as I type this. I do recall having these pins bottoming on my motor but hell, I'm old and forgetful.
Does that hole have a flat bottom?

Thanks for the reply. Yes it has a flat bottom. I don't get why the hole is deeper and of course I'm loathe to drive the thing in for fear I can't get it back out again.