Getting worried - I have a flight into Tokyo Haneda on ANA that arrives at 21:10, and have booked a separate flight flight to Saigon on JAL that departs the next morning early at 1:30. These itineraries were booked separately several months apart.

I understand transiting through Japan is allowed, but will I be denied travel at check-in without a valid Visa since the flight I would be checking into has the final destination as Tokyo? In other words, since the connection to Saigon is not on the same ticket, will I be denied boarding to Japan?

If I am allowed to travel, I believe Haneda allows overnight layovers, and this itinerary will be possible... but this would not be possible at Narita since the next flight is the next day. Is that correct?