I'd call it more of a hunch based on the fact that Johnson didn't seem to know anything about the principles of the party whose banner he's running under. I can't quite call it a conspiracy theory because in order for a conspiracy to take place the two would have to be planning on committing an unlawful act. This, at it's best seems merely a deceptive act.
Perhaps there is some illegal and undisclosed campaign funding but I'm not money smart enough to go down those rabbit holes. The ideas you mentioned seem plausible. I'd expect there would be secret contracts with non-disclosure arrangements laid out which specify exactly when the candidate will endorse the party member favored by the individual (or group) that's providing the funding.
RE: Gary Johnson Could Have Won His Senate Race If New Mexico Had Ranked Choice Voting