While I love Atlantis and Treasure Planet, they also flopped massively. The thing about unions is a valid point and does suck a lot, but sadly I don't think Disney would have made another film like these anyways.
Take this with a grain of salt because my memory is fuzzy and I just read it in a comment somewhere.
The reason Treasure Plant flopped was because Disney wanted it to fail to use it as an excuse to shift to 3D. They barely marketed the film and released it in November, which meant it would be competing with the Christmas films. And when the movie had won an award, no one was there to receive it cause they weren't expecting it to win anything.
The movie actually used a lot of 3D animation in combination with its traditional 2D animation. I don't think they made a movie fail intentionally to excuse a shift to the very technology said movie employed a lot more than their prior ones. If anything, the knowledge gained during the production helped them for sure.