Plan the back rooms for the machine shop with 10' ceilings and the residence area above it, and that will put the ceiling in the main room bays high enough for a car lift - or two even.
And don't discount a Lube Pit on one side - much cheaper than a second lift, and better for some things because it's moderately idiot-proof. If you want fully IP Rated, leave a lip and cut a bunch of 4X8 planks to close it off flush when you have company.
Don't forget the sump pump & drain to outside (and a bucket to trap any oil...) and semi-permanent exhaust ventilation (gasoline and other flammable vapors settle, so put a pickup at the bottom to outside with an EP bilge blower fan...) and outlets for power water & air in the pit, so you aren't running cords and hoses on the floor. I'd just run a 4" DWV under the floor slab to the wall, and you can snake it through later as needed.
14' high door on the lube pit side, so you can nose in a motorhome or truck for an oil change or alignment. If you put in a normal 6K or a light truck 10K or 12K post lift you may want a big door on that side too.