Yes, the light switch is usually wired to just turn on and off the ceiling mounted outlet that the garage door opener plugs into. As a side note, if you have kids etc. you might want to mount the garage door opener switch up higher than normal or in a strange location so you don't run into the problem of the switch accidentally being flipped by someone else while you are out and then you not being able to open the garage door when you get back home and want to park the car in the garage.
As my attached picture shows, the tracks can easily follow the angle of the ceiling instead of running horizontally. It is not a big deal to do.
I don't know if I understood you correctly or not, but if the angled hip ceiling for the garage's side wall (adjacent span) extends into the up-sloped ceiling track area (under the main span) for the garage door then you would have some issue. You would then have to make the lowest point of the ceiling (adjacent span) become the level the other garage door track runs at which could eat up some of your lift headroom.
NOTE- If you decide to install up-angled tracks like the ones in my picture, think seriously about installing automatic track slide locks (that pin through the door track when the door is all the way up) for the garage door. I am not sure if this something regularly done for this type of track layout or not, but they are commonly used for the door when it is in the down position to help prevent break-ins. The reason is, a regular door lays horizontally when up so if a torsion spring ever snaps the door will most likely stay in place, but with an angled door track (depending on the failure) it could drop like a rock and possibly injure someone severely if automatic slide locks are not activated when the door is in the up position. Jackshaft doors usually come with one set of these already(for the down position), so you shouldn't need to add a second set, just wire the regular set so it also engages a second track hole when in the up position. Most likely no more money for parts, just a couple minutes more wiring, some drilling of new holes into the track, and some extra planning so all the hole locations for the slide bolts are in the right spots.
The other thing is, depending on your particular installation you might lose the ability to easily open the garage door manually. A garage door set up like this is not as easy to balance with torsion springs, so it might not want to just stay in place on its' own when up without the jackshaft opener motor holding it there. If the torsion springs are set up to hold the door in place when up, they would most likely be pulling way too hard when the door is down which would cause the door to jump several feet up on its' own if you disengaged the opener motor, so it is sort of a pick-your-problem situation. If you only intend to open the door with the opener motor the problem is not much of an issue at all.
There are some failures associated with the automatic slide locks not disengaging as they should and then damaging the jackshaft motor when the garage door is being opened. That is a risk you have to be willing to take with a more complicated setup. It would be a safer setup having the slide locks, but there is an increased chance for a costly opener motor failure if they fail to work correctly for some reason.