If you decide to stay near the airport, I would not let the above worry you. Although it may be good advice in general, it doesn't apply to your proposed situation. First of all, the Narita Express is not a commuter rail, but is designed solely for airport users. Although there is nothing to prevent a commuter from using it, its cost makes it likely that it's not used very much for that purpose, and in any event, all seats are pre-assigned and there is dedicated luggage storage in each car, so there will not be crowding or luggage problems even during commute hour. Secondly, the transfer between the N'EX tracks and the Shinkansen tracks at Shinagawa Station is likely to be among the easiest you could have, and also will not be plagued with sardine conditions in the carriage. Also, consider that your Shinkansen departure would be against the commute direction.