Yes. It is a completely different piece. It’s just a large piece of webbing with a pocket and four ends that attach to the lifting platform. So, yes, you can have it set up prior to backing your truck in the garage.
You do not need the rear window up when you lift the top. You will briefly have to open it up a little just to get the webbing to the hooks.
My garage ceiling is 10 feet and I have no issue parking my Bronco under it with it directly over the hood. It has a good 4 feet. You should be OK.
as a...
I use the standard 1 inch spacer in the front by rough country. It works amazing. Installed and aligned.
I used the 1 inch spacer from rough country. Installed and aligned. Works perfectly with my HOSS 3.0.