You may travel without disembarking and pay for only the uncovered section (at least with JR West)
- You do not need to disembark.
- You must buy extra tickets for only the section not covered by the pass.
- You must exit the destination station via the manned gate and show your rail pass together with your tickets.
- It’s not clear whether the manned gate must be used at the origin, but it should be safe to use it anyway.
- For limited express, the tickets must be bought before boarding the train.
- For a regular train, you can still buy the tickets before boarding, but the train may also be boarded without the extra ticket and the missing fare paid at the destination (although this might be possible only if the origin station is within the pass validity area).
Also, contrary to the doubts expressed by several users, this particular pass is indeed valid for all limited express trains within its overall validity area, rather than only the several examples named on the website.
Full story and source
This was intended to be a general question with a specific example, with the hope that the policy is publicly documented somewhere for the whole JR group or for each company separately. Unfortunately, this seems to not be the case, as no such policy has been produced in an answer.
I ended up submitting a specific inquiry using a form on JR West’s English-language website. I asked:
<The pass or ticket name you would like to ask> Kansai-Hiroshima Area Pass
Is this pass valid on all limited express trains or only the ones named on the pass description page (Haruka, Kuroshio, Thunderbird, Kounotori, Super Hakuto)?
Is it possible to board a train on a station within the pass area (e. g. Kurashiki), ride it all the way to a station outside the area (e. g. Matsue), and pay only for the portion not covered by the pass? What is the correct procedure for doing this on a regular train? What is the correct procedure for doing this on a limited express train? (For example: should I simply buy a ticket from Soja to Matsue? Should I visit the green window at Kurashiki? How do I exit the station gates at Matsue?)
I got a response by email in less than a day. The relevant excerpt (in good English, unedited except to add emphasis):
We would like to inform you that the Kansai-Hiroshima Area Pass is valid for all Ltd. Exp. trains (non-reserved seat) in the valid area and the Shinkansen (non-reserved seat) between Hiroshima and Shin-Osaka.
As you know, “Matsue” is not included in the valid area of the Kansai-Hiroshima Area Pass. As for your journey from Kurashiki to Matsue with this rail pass, you are required to pay for the uncovered portion additionally.
For example, if you are planning to take the Ltd. Exp. YAKUMO (non-reserved seat) from Kurashiki to Matsue, you need to purchase the additional tickets at the JR-WEST ticket office before you take the train. The price for the additional tickets is 5,280 JPY/ one-way per adult. The breakdown is as follows.
-Basic fare ticket from Soja to Matsue : 3,080 JPY
-Ltd. Exp. ticket for a non-reserved seat from Soja to Matsue : 2,200 JPY
When you purchase the additional tickets, please make sure to show your rail pass.
At Matsue station, please use the manned ticket gate to show them.
On the other hand, if you just take Local trains from Kurashiki to Matsue, the additional fare you need to pay is 3,080 JPY (basic fare ticket from Soja to Matsue )/ one-way per adult. In this case, you can pay for the fare when you arrive at Matsue station. Please visit the manned ticket gate and present your rail pass to our staff.
(They also recommend the San’in–Okayama Area Pass as it is cheaper than the extra tickets for a one-way limited express, in addition to the above explanation, which is much appreciated.)
This is not the fully general answer I had originally hoped for, but it very clearly explains the situation for the particular Kansai–Hiroshima pass, and I’m going to assume the same policy applies to other passes. However, it may be wise to send a similar inquiry if another train company’s pass is involved.