Earlier quoted context omitted.
Can you elaborate a little on these devious ways?
The basic principle is that your advisor has control over everything , and you have control over nothing . Need an important collaboration for your next paper? That won't happen without your advisor's support. The same goes for access to specialized equipment or supplies (the budget can become very tight when your PI doesn't like you). At most schools, your PI also controls your funding; you can expect to TA more oft…
So, ultimately, if your startup-company moonlighting starts to eat too much into graduate research time, you're going to have to fish or cut bait: Either keep your adviser happy, or take the necessary leave of absence.
Note that (most) graduate advisers are not evil people. I suspect that many of them will quite happily grant you six months off to pursue your startup-company dreams... if the timing is right (hint: don't ask until just after the Nature article is submitted) and after they explain to you that your publication record and your graduation time will be set back by a year or more. Oh, and you probably won't be given the plum projects ever again, since your adviser knows that you have one eye on the door... those are the breaks of the game.
One very special caution: Your adviser may try to enlist your help in his startup company. Be very wary of this situation, or of any potential adviser with a history of this. You want your adviser to be unambiguously focused on helping you graduate and get a better-paying job... or as unambiguously as possible, anyway.