The shiny cylinder is supposed to be seen. This is a big blue box desperately hoping not to be noticed.
Hoping an issue is not noticed is never an effective design solution and there were plenty of alternatives. Alton Towers has repeatedly shown how good roller coasters can conform to a very restrictive maximum height. The box could have been depressed (yes, it is possible to go sub-grade in central Florida). The building could have been given a simple finish and unique form that follows the pattern language of Future World without being a tarted up box shouting “Look at me!!”
There is a reason almost no ride (with the exception of Transformers, and that was a hold-over from California, and the underground is maintenance) has underground portions in Florida.
Disney has previously brought the "guest level" up instead. Dinosaur, American Adventure, and quite a few others bring guests in on higher floors in order to "shrink" the building. Dinosaur is a great example, as that building is 2, 2&1/2 stories. But there's nothing to see in terms of showbuilding, since you're on the second story already.
The issue with this this solution for this building is that there's 1) no guest area directly connected to it and 2) an already-built future world sitting just above ground level.
Now, say they did want to build their very first subterranean roller coaster and sunk it a story, two stories down. This coaster has a massive footprint - one of the largest pours Disney has done. The removal of the dirt alone would be prohibitively expensive for an already expensive project. Not to mention the thousands of man-hours that would now need to be put in to engineer solutions to all the problems that would arise from the building being built below the water table. Reinforced walls, protection from flooding, pumps to get any water out that may get in - just a nightmare. Maintenance would constantly have to worry about an increased risk of flooding and water damage, alongside the upkeep that normally comes with coaster operation.
Finally, a themed building. This would be unique, as it'd be something that could be seen from half the park. Using "abstract geometry" and "a simple form and finish" may not be enough for a building of this prominence. Even the solution of painting it right now has found that a single color isn't even enough.
Going the themed route would be difficult - you'd have to find something future-worldy enough, but also not anything that would be too crazy while in the World Showcase. You'd also have the issue that the majority of the building is covered by other buildings and shrubbery while in FW. Really, the best views of it are in the parking lot and on the opposite side of the world showcase. So they spend all these resources theming a building when the theming can only be useful from a distance.
I'm certain that this was their best choice - again, outside of not building it at all.