PS I'm not familiar enough with this assy. but if the flywheel comes off (albeit with a bit of effort), could the (very precise) clearance hole not quite line up with the threaded hole in the crank, thereby creating the flattened threads ie when you try and screw it in the bolt rubs on the "clearance" hole??
I thought I'd posted my theory but it isn't here.
If the flywheel is a tight fit on the crank, and I think it has to be, the bolt may have been forced in when the flywheel and crank holes were slightly out of line. Sadly, if one bolt is knacked from being out of line, the others may be as well.
. I imagine that the bolts should be located, (but not fully tightened yet) in their threads when the flywheel is still hot.