Ikar, I never booked intercity travel in Japan whilst I was in a wheelchair, and I’ve not needed a chair for over ten years.
All I can say from that time is that the services I received were excellent, but very hands on and a little “faffy” and laborious on the part of the employees who had to deliver it. Everything took longer to do and get done than when not using a wheelchair.
I just saw this recent blog post which illustrates what I mean (little seems to have changed)
Shinkansen & Japan Rail Pass as a wheelchair user | Little Miss Turtle
The part I’m referring to is where the blogger goes to a JR service center to reserve a place and the procedure takes 40 mins as phone calls need to be made.