I'll have to check with Michael Broggie, but I don't believe that Walt specified anything about the WDWRR other than that there was to be one. Walt died in 1966, and Roger Broggie didn't acquire the locomotives in Mexico until 1969. I do know that Roger suggested using larger narrow gauge engines because of the 2% grades they'd face.
It doesn't seem likely that Walt would have specified standard gauge. Disneyland and the Magic Kingdom are built on a variety of scales, but most of it employs forced perspective. This was something of a necessity in Anaheim because there's wasn't enough room for full-size structures. But, even if there was an abundance of land, Walt wanted an intimate feel for the Parks; something that wouldn't intimidate children. The Magic Kingdom does have the luxury of space, and it's reasonable to assume that Walt would have utilized some of that to avoid the crowding experienced at Disneyland. But it's hard to imagine that he'd allow too many "real world" dimensions in the Park, and standard gauge trains might have felt too big, and therefore too ordinary, for his Park.
For example, the C. K. Holliday, if it were built to standard gauge size, would be 19' to the top of the stack. That's a fairly big engine and -- while pretty -- wouldn't feel quite as "magical". Cinderella's Castle dwarfs Sleeping Beauty's castle, but is still much smaller than a "real life" castle such as Neuschwanstein.
As for the Matterhorn, I'm sure there's a story behind its obvious omission from the Magic Kingdom. While Florida attractions such as POTC and the Haunted Mansion are not carbon copies of their West Coast counterparts, the fact remains that they are there. The Matterhorn opened in 1959 and was very popular at the time they designed the Magic Kingdom. So, why isn't there a large bobsled-style attraction at that Park? That would be a good question for someone like Marty Sklar or Bob Gurr.
Personally, I don't doubt Walt would have had a place to sleep at each of the Parks he built. This would have been more a matter of practicality than privilege: his apartment at Disneyland wasn't built to entertain guests, but as a place for him to sleep when he'd put in 18+ hour days at the Park. The Royal Apartments above POTC would have been better suited for entertaining guests, but the primary driver continued to be a sleeping place for the man who was always working. In that EPCOT was intended to be a residential community, it stands to reason that he'd have a residence there. But, this would have likely been in addition to the Castle suite, not instead of it, because EPCOT would have opened years after the Magic Kingdom debuted.