Originally Posted by
angra
I can't say about the faux pas part, but I did exactly what you propose on a recent trip. I don't ever bother with Green Car, except that one trip, I was traveling with my father and felt like a mild splurge. We hopped on to green cars without reservations the whole trip. On some of the trains, there is a SUICA point at the seats for you to pay the green upcharge. Since we had the pass, we didn't do that, and the conductor came to check our pass each time, but otherwise it was exactly like the non-green.
Sounds like you were using the green car that was attached to some medium distance commuter trains, which are first come first served, you can purchase the seat by touching the suica reader with a suica card, if you have a JR pass, the conductor will change the light above to note the seat is occupied after.
However, on the Shinkansen and limited express trains, the green car is reserved seating only. The conductor goes through each car with their tablets, so they know which seats are reserved already, if they see someone sitting in a seat that hasn't been reserved or reserved later down the line they will check to see if you have a reservation.