Valve Cover Bolt fails to bottom out....

If nothing has changed and those are the bolts that came out of the head, I would suspect that oil got in the bolt hole and partially filled the hole with oil. Oil is not compressible, thus the bolt goes partially into the hole and stops. You can check it with a Q-Tip. Stick a Q-Tip into the hole and if it comes out oily, keep inserting new Q-Tips until the hole is clean. 0.02...
That's a good print....I will check it out.