A lot of dealerships aren't hard wired for sorting what is essentially a motorcycle rear swinging arm or fork & rely on the stampings either side adjacent to the slot for the rear axle.
Setting the rear wheel to run in the same plane as the fronts is fine with just hand moving, and once in the same plane, will not matter whether at the bottom of the travel or the top.
The belt tension will, and this should be done with the car standing, so you'll need space underneath unless you have small arms..!
Professionally, you'd be well advised to find a company or engineer that is used to the breed. It's going to take them time to get their head around things if not, and that time you'll pay for.
It's not rocket science, just patience and method.
Don't over think it..
