Originally Posted by
JALOO5-Flyer
I'm dumb enough that I have never taken Shinkansen before, but from my experience on local trains, my understanding of the "multiple fees" is the "extras" like limited express ticket or seat reservation ticket etc.
It can confuse a lot of people when they first take train rides in Japan.
There is a base fare by distance, there is then an uplift for riding the Shinkansen. It is phenomenally more expensive to build, maintain, and operate than normal trains, so passengers on the Shinkansen are charged the cost of the operations rather than having the lines cross subsidised by the regular lines.
The convoluted part is not understanding it, the convoluted part is understanding it from the English descriptions that JR writes, especially if you read the descriptions and limitations on the JR Rail Pass. That is an area where Japan is still struggling, writing clear and simple instructions in English.
On the topic of JAL online check in domestic, I need to test it next time I fly domestic, I never do online check in, so I can't really chip in with views of that.