I'm with John on this, the bolt threads are definitely "decapitated" by something in there, but is it just something hard stuck in a thread or are the threads damaged inside, the only way to be sure is removal of the flywheel, but that sounds quite a big job for the uninitiated like me! So my first thought would be to clean out the threads as you want to do, but if the tap doesn't fit and a bolt does, use a high tensile bolt if possible and cut a slot down the threads and use it to clean out the crank thread, this approach has often been a good fallback to clean up threads in general if a tap isn't available.....have to say I'm surprised though that the access hole is sized soooooo precisely to avoid a tap going through!
Good luck Mike....
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??