You're underthinking it.
The song is about Bowie's fame. He had achieved a certain level of success and he had to step out of one personality and style, his capsule, where he was safe but no longer inspired - the circuit's dead, and into another.
Major Tom later becomes a reference to the addiction of that success and fame. "To get things done, you'd better not mess with Major Tom" is expressing that if he wants to achieve what he wants to, artistically, he should not make choices in the name of popularity or fan service.