Since the Japanese authorities say that they have no records of her being in custody and she presumably knowing that she would be a person of interest, might she have been inclined to give a false name?
It's all apparently muddled up in confidentiality which is frustrating as the events were 80+ years ago.
The Marshalls are pretty far away from Japan, and so were cut off pretty early. They were also the site of heavy fighting (unlike, say, most of what is now FSM) so it's easy to imagine paperwork preservation wasn't a high priority.
They claim to have been told to keep it quiet by the US Government
A government with a track record of not caring to care for citizens that get in trouble over seas. Especially back then
They could have wanted it "covered up" just to avoid dealing with it or concerns over international incident.
It could be hogwash, all built around rumors:
https://pacificwrecks.com/aircraft/electra/earhart/
http://www.ameliaearhartmovie.com/briefcasefoundinsaipan.htm...