MacArthur deserves a bit of understanding, if not sympathy. He was going to take over a country whose leaders had surrendered under extreme duress (two A-Bombs). But the Japanese people still considered the emperor to be god, and were fiercely loyal to him. One word from him, and the U.S. military would have faced a revolution and had to slaughter millions of civilians or be overrun and killed. So, yes, Mac made deals with the Emperor's faction, the major one being to allow Hirohito to remain in power, though he had to renounce any claim of godhood. I have no idea where the removal of the imperial crest (actually the family "mon" of the emperor) came from, but I suspect it was of Japanese origin, part of the process of "saving face".
As others have said, there is probably no definitive answer to the many questions. But if American troops were ordered to grind off "mums", there would have to have been a written order to do so, and thousands of copies made; I know of no such order. Further, the loss of face occurred when an enemy infidel touched the imperial symbol; once it was in American hands, the dishonorable deed was done; it would have been too late to prevent it.
Regardless, it is pretty safe to say that Harry Truman was too busy to keep track of all those Arisakas and have the FBI grind off the crests. That vet just might have been fibbing a little.
Jim