I had the same thought. However, when I was exchanging my voucher for my JR Pass and reserving a seat on the Shinkansen to Kyoto at the exchange office in Shinagawa I asked if I could reserve a seat with luggage space as per the new rules, the staff member wouldn't let me. He gave me a tape measure and asked me to measure all three sides, and when that showed it was <160cm he said I wold have to put it up in the overhead rack. Getting the case up there was an experience I don't want to repeat! I noticed the row with luggage space in my car was empty the whole way.

On the way back I used a ticket machine to reserve my own seat and picked a seat with luggage space. I was the only person in the row.