I had a look at every image I could find of the Yokosuka E14Y1 and all are depicted in national insignia with no mention of devious marking changes.
If they didn't do it for Glen then I can see no reason why the Sieren would be any different?
Myth busted? The most quoted source in the wiki article that mentions the "documentary" is Air International October 1989. Not one mention in that article of insignia changes. Personally I don't think the Japs would go for it, despite being the bastards that they were...