I’m not even going to say how much we spent on airfare to Japan. When it comes to Disney, it’s a 3 hour flight and we can manage with economy. 14 hours to Japan is just not something we can do anymore (I could in my 20’s but sleeping funny wrecks my body for days & my husband is 60 & 6’3” so cramming into economy is a no go).
I think Japan is cheap ish if you are traveling with 2, but once you have kids over 12 years old they are ‘adults’ so you have to pay up for apartment hotels for all or get 2 rooms at regular hotels. Not like in the US where you can always fit 4 in a regular hotel room. We are at the Sheraton Hiroshima right now & had to get 2 rooms for about $190 each per night.
We have a ryokan in Matsumoto for 1 night and that is $1000 for the 4 of us. It does have a private onsen (teens won’t try the shared bath) and includes dinner & breakfast.
We flew Zipair with lay flat seats, other carriers would have been several thousand more for a comparable seat. Like I said it was the most expensive part and mostly unavoidable unless you do fly more low-cost (zipair is already considered a budget airline).
As far as economy my husband is taller than yours, exit row seats we have done to Europe in economy to help with that.
Japan is quite inexpensive overall though when you're looking at what you can do once you get there. You're correct about the hotel situation because in Japan most beds are twin sized and may only have one bed in the room depending on the hotel. The costs however, even if getting two rooms doesn't have to break the bank. $190 is quite a good price, like I mentioned in my comments our other accommodations cost $100-$200 per night. That's not really easy to get on-site Disney (if comparing).
As far as comparing flight time....well yeah...but that's not the point nor the point for the article writer who flies from Australia. I can get to a lot of places being in the middle of the country fairly quick but it doesn't make it actually cheaper. If I were to use flight time and overall experience domestic travel is more expensive than international travel all things considered (distance to location, what the location is, etc) and that's just flying SWA. For international travel unless flying on ultra budget carriers you also get food.
As far as your ryokan costs, typically they are the most expensive accommodations you can get in Japan, ours had a private bath on the balcony food also included as well as having first come first served several private baths in actual onsens and then several shared ones as well; we chose to use our private bath on the balcony instead. 2 rooms would have still costs us several hundred less than you spent although our room had two twin beds and a separate eating area and was quite large. Ryokans vary in costs and season as well as location. But again as I pointed out in my comment it was the most expensive outside of Disney, I already spoke to that. But you don't have to stay at a ryokan either, but it can bring more culture to it. FWIW our hotel in Takayama was technically an onsen though I didn't use it.
This is getting off topic for the thread but my crux of my comment is that hearing Japan often makes people think it's super expensive but for the most part (and I stress that) the airfare is the bulk of your costs. To go to WDW on a 10-day non-park hopper would cost close to $1400 for two people, we never spent anywhere near that on all of our activities in Japan, not even remotely close, including the Tokyo Disney tickets.