I had noticed that, but wasn't certain that the guy who machined your safety had necessarily milled the cutout in the right place; all those B-29s overhead were probably a bit distracting.
I've never taken down the bolt on either of my Arisakas; looking at the instructions I have, it's hard to tell how easy it would be to reassemble incorrectly.
A Collector's Guide to Military Rifle Disassembly and Reassembly by Mowbray & Puleo indicates that the cocking piece/safety will only install one way, but who knows how that may be altered by manufacturing shortcuts on these late guns. Can the cocking piece be turned enough to remove it?