I have addressed this issue slightly differently. As others have said, setting your levels on the tripod without the head on it is the way to go. But that can become tedious. I decided to make my mount/scope mobile so I can wheel it out of my shed and place it on marks I have previously made on my concrete apron to represent a South Polar orientation. The whole arrangement sits on a wooden frame with big castors and wind down some legs I have made which hold the tripod firm and keep the castor wheels off the ground.
I then use Sharp Cap to do a polar alignment and because I have marked the locations for the tripod legs, I rarely have to do another alignment.
Here are some images that may give you and idea of what I have done.
Peter
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