Our garage doors haven't been installed yet and I just realized that they will be covering nearly half the ceiling when open.
If you think about this a little more, it may not be a problem for you.
You only
need light on the back half of the garage if you are doing work in the garage at night/dusk with the door open.
If you live in a cold place, you aren't going to do this because you'll be closing the doors to keep the heat in. If you live in a warm place, you aren't going to be doing this because you'll be closing the doors to keep the bugs out. (There are also nudist mechanic scenarios, but hopefully that's not an issue here.)
So, I don't think you'll really miss those lights for the short time the doors are open unless you plan to work in the garage on warm days with the doors open and put up some sort of screen material over the openings.
Some people put windows in their doors partly to let light come down while the doors are open. Also, if you go with a high lift track (if you have the ceiling height) the door doesn't come out in to the room nearly as far as a normal track and it may not even cover your light. (depending on placement)