Well, I found a photo of the caboose at Disneyland Tokyo from a better angle:
When looking at the photos in the first post of this thread, I'd say they are two different cabooses. The one we're claiming was in Western Mura looks like the body of the car hasn't been too changed/modified from the normal appearance of a narrow gauge long caboose, whereas the one at Disneyland Tokyo has been remodeled twice since leaving the narrow gauge motel. For example, the one at Western Mura has the metal shades above the windows (if that's the correct term for them) and has the bottom of the chimney for a woodstove still sticking out of the roof. On the one in Disneyland Tokyo, those details have been removed by Heritage Square/Magic Mountain which was when the cupola was moved, more windows were added and the original interior was removed for more seating.
This thread appears to be 4 years old, so hopefully this info hasn't been discussed already somewhere else