Even ignoring the issue of there having to be a fixed ship time, why would the ship's orbit matter? The day/night cycle in the ship is artificial. Even if a specific away mission could be planned to such a degree that you could sync the timezone in advance by gradually altering the ship time, the physical location of the ship would never matter.
Also, I strongly question the assertion that jet lag would be worse with transporters. Yes, if you just suddenly appear in a different time zone your daily cycle will be out of sync, but it won't be any more out of sync than if you just spent several hours getting there - your body is still expecting it to be noon at 9pm. Jumping from daytime into nighttime shouldn't be more disconcerting than being indoors and having the lights go off suddenly.
Indeed, one of the contributing factors to jet lag is the fact that flying is itself uncomfortable and somewhat stressful for most people, so your rest is disrupted by more than just the time zone difference. Transporting should at least partially eliminate those factors (though, of course, being on a dangerous away mission won't help).
I suspect that the main reason Starfleet personnel don't suffer from jetlag when transporting is because they are medicated to counter it. There have been multiple instances on the shows - especially TNG - when Starfleet doctors have demonstrated the ability to directly manipulate neurological patterns, far exceeding anything we can do now. I'm guessing an "you're on a 27-hour cycle and it's now 15:00" pill is a triviality for them.