Many of those stories seem to have begun when folks began to realize that a ground crest meant a surrendered rifle. But a lot of vets had already told tales of how their souvenir rifles were captured in hand-to-hand combat, so they had to quick invent a story that would explain how the crest was ground.
A common one was that Roosevelt/Truman/MacArthur/Nimitz ordered Americans to grind the crests aboard ship to avoid offending the Japanese. (That was still in the middle of the war - we were killing Japanese but couldn't offend them!!???) Another was that Japanese units carried grinders with them so they could remove the crest before engaging in a "last ditch" battle. (This is a variation of the "bayonet and rock" story.) I heard the "Harry Truman" story from only one vet, but he was so convincing that I could see someone believing it.)
In truth few Japanese rifles brought back were actually combat capture, and even fewer were brought back by the men who captured them. Mostly, the Marines or soldiers who had picked them up on the battlefield from dead Japanese (very few Japanese soldiers surrendered), sold them to sailors on the ships who had the means of bringing them back. For most of the war, troops who had captured one island were shipped on to the next and were in no position to carry two rifles. (And no one was going to throw away his M1 and keep a Type 99 souvenir for fighting!)
Only after the war, when American troops were sent to Japan were large numbers of souvenir rifles made available to Americans, and it is those rifles that are in American collections today.
Handguns were another story. Smaller and easier to carry, many combat captures were tucked into a duffle bag or mailed home (prohibited, but it was fairly common). Of course, many more were also surrendered after the war, but not having a "mum" to grind off, it is not so obvious.
Jim