I didn't have any issue last night whilst flying out of Narita.
I stopped by the Z counter and explained to them that even though I had the electronic boarding pass, on my previous flight they had suggested I better visit a check in counter anyway to avoid again being called at the gate to explain why I was flying out on the 2nd leg of a return ticket to a country of which I am not a citizen of. The girl serving me just pointed to the BP on my phone and said you're good to go with that.. She barely even looked at my passport and I don't think added anything additional to my record.. then at the gate was no issue. So.. not really sure. Maybe just at Haneda they are being a bit more strict these days.