I routinely fly ANA from Japan to a UA hub in the USA and then connect onward to BOS on UA.

I've always been able to check in online or on the app. All itineraries are 016 ticket stock. Sometimes the NH flights are booked as "proper" NH flight numbers. Sometimes as UA codeshares. Sometimes the UA domestic flights are booked as NH code shares. Sometimes it is a mix.

I've never had an issue.

Usually when the itinerary is ticketed at the time of purchase, I always go to ANA Sky Web and view my itinerary with the Amadeus record locator. And I always put in my passport information, and any other info they need.

If everything is properly registered, ANA will automatically check you in 24 hours before departure. I get my ANA boarding pass, as well as the onward boarding pass on UA.

Again, I've never had an issue. Perhaps its always because I'm checking in Ex Japan? Or maybe because I've got all my passport / passenger info in Amadeus before checkin?