I think part of the confusion comes down to the painstaking efforts of WED to hide other out-of-theme areas from being visible. Seems weird to let the train be visible when it would break immersion. It's better to think of the train as the constant thread through the whole park, similar to the RoA or the steamboat.
This to me is one of the great misconceptions of the contemporary perspective on Themed Design - that placemaking is only as good as it is insular.
Disneyland and Magic Kingdom, two of the greatest themed design efforts in history, both frequently, intentionally, and successfully buck this rule. Anyone suggesting that the Train "breaks the immersion" of Tomorrowland is missing the point. At Disneyland the Train has been visibly passing through Tomorrowland since Opening Day and stopping in it since 1958, and at Walt Disney World there has (until now) always been a prominent stretch of track during which the train was consciously shown off rather than hidden. As Martin says, it was intentionally visible in front of Space Mountain. These were no accidents, they were intentional - as you said, the Train is meant to be a thread that strings the whole park together.
By this standard, Sleeping Beauty Castle is placed at the end of Main Street only because Walt Disney didn't have the resources to mask it off - but we know this isn't true, the Castle's placement at the end of Main Street was half the point of the park. Same with Cinderella Castle, which takes things a step further and is intentionally visible from every land in the park - the presence of the Castle is not an example of Thematic Intrusion, its juxtaposition is purposeful and serves a point higher than the "immersion" of any one land. Who ever looked and said "oh man, I really thought we were in a Space Port until those Medieval Spires ruined the illusion"? No one, and you're not really meant to. Ultimately, before the park is Tomorrowland or Main Street or Frontierland, it is The Magic Kingdom.
This is even more true at Disneyland, where the Monorail, Train, Matterhorn, Skyway, Castle, and more all do (or did) run through or past eachother to a spectacular effect that would never meet the standard of "immersion" where unrelated properties and periods are screened off from each other. The intermingling of these elements has always been one of the great strengths of Disneyland - a feature of its mission, not a liability against it. The purpose of the Berm was to keep the world from intruding on Disneyland, not to keep Disneyland from intruding on itself.
There are, of course, things that SHOULD be masked - unthemed showbuildings should of course be hidden, and things like Rapunzel's Tower are examples of actual thematic intrusion because the view of it from Liberty Square was simply not accounted for in its design - its visibility from there is purposeless. But conscious, considered design can successfully place elements from seemingly disparate stories together to create a new one - the story of the greater Park. This is what WED was doing, and what the current ethos of Imagineering frequently fails to recognize.
That attractions, lands, and even parks are now typically designed with a different methodology is fine and legitimate - there are a number of things built to this end in the last 20 years that achieve spectacular results in this style. But that is a relatively newer approach in the lifetime of the medium. To suggest that Disney themed design has always been in a race towards this end and merely fell far short back in the day is both to retcon what was actually happening and miss the great, great successes of that earlier approach. People have ALWAYS felt immersed in The Magic Kingdom and Disneyland, but that's not DESPITE the presence of a Castle at the end of a turn-of-the-century street or a steam engine in Tomorrowland, it is much more BECAUSE of it.
These are places where "anything can happen", as long as they stoke the imagination rather than ruin the magic. The Train does the former and not the latter.
