Does JR really cover all other passes?

Hi Japan-Guide,

I would like to ask, whether the Nationwide JR Pass really cover the other Region Passes.
Here's the plan (visiting period around May 2023) :
From Tokyo i want to go to Kawaguchiko (maybe Fuji-Q too), Shibazakura and Alpine Route. I'll spend 3 days for these places, i'm buying JR Nationwide, but for Kawaguchiko there's Fujikyu line to buy from Otsuki Station. But for Fuji Hakone & Mt Fuji Shizuoka Area pass are covering Kawaguchiko station, can you please explain it more detail about the covered area for JR Nationwide? Especially tourist attraction around Mt Fuji.
Thank you.

Regards,
Erna

No, it doesn't! There are many regional JR passes that cover trains that are not covered by the nationwide pass.

The nationwide Japan Rail Pass does not cover the Fujikyu trains between Otsuki and Kawaguchiko and it does not cover the Alpine Route. The Japan Rail Pass generally covers only JR (Japan Railway) trains as explained here:
https://www.japan-guide.com/e/e2361.html

In order to find out whether a train is covered or not, you have to find out whether it is a JR train or not.

To complicate a little further, there are a small number of JR trains running on non-JR train lines (which are not covered by the nationwide pass). Among them are the direct JR trains between Tokyo and Kawaguchiko (which are not covered between Otsuki and Kawaguchiko). Some other prominent ones are listed here:
https://www.japan-guide.com/e/e2368.html

Thanks for your reply Uji-san,
So if you can suggest to me, which additional passes i better buy in order to get to Kawaguchiko, Shibazakura and Alpine route? Should i just buy the regular additional tickets on site?
I've been reading about the Rail Passes for a few days now, but still not sure which passes to choose to keep me from over-budget my train expenses.

I figure that Fuji Hakone Pass does cover this Fujikyu Line, and for Mt Fuji Shizuoka Area Tourist Pass cover the Fujikyu Buses to Kawaguchiko, but i'm not sure if any of this two cover the bus to Shibazakura matsuri.
As for Alpine route, the extra fee for cable car and buses is un-avoidable i guess? Can i only go to the snow tunnel between Bijodaira to Murodo, then get back to Toyama?

The Fuji Hakone Pass is an offering from a different company - Odakyu. They have hundreds of companies that they look after, many around the Hakone/Fuji area that are all owned by them, but they do a stack of other things too (they run my local city buses as an example).
I suspect you should have queried if the National JR covers all the other regional JR passes, which it does except for some special cases. However, more generally, it does not cover the passes from other major companies like Tobu or the above mentioned Odakyu.
Generally, the exceptions on the national JR pass would be specific routes (like Otsuki to Kawaguichiko where a special arrangement exists for some train/ticket combos - as mentioned in the pp), other times there could simply be a surcharge collected on the train while riding. I do recall years ago a group of helpful JR ticket agents stressing about a trip I was doing that used some non-JR track and that there would be a huge fee - turned out the "huge" fee was 210 yen.