Yes, but it's better.
Because the monorail without overlay is WDW transportation. The monorail with overlay is a gigantic billboard. Without overlay, it is what it is and it gets its job done without calling attention to itself. With overlay, it's equivalent to sticking a gigantic blinking sign on the monorail that says, "Hey!! Look at me!! I don't fit in!!"
It's also relevant that one of the primary purposes of Disney World as a whole, from its inception, was to demonstrate futuristic transportation systems. Thus the monorail, by virtue of being a monorail, is relevant to the WDW resort. The Avengers has jack to do with anything in WDW other than the fact that they're both owned by TWDC. It's synergy/marketing for its own sake with 0 attempt at theming.
And no, it really doesn't fit in the Contemporary. Whether you go with the original "Grand Canyon" theme that's only still upheld by Mary Blair's mural, or the newer sleek, ultra-modern aesthetic, the classic monorail design is a better fit.