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Unsure about Alt-Az tripod mounts, but the initial tube position of a Skywatcher Goto dob makes no difference to the alignment (that I've found) when you turn it on and begin the star alignment. This is when using the hand controller at any rate. I tried having the scope level/north facing for a while, then discovered it doesn't really matter.
I've found when using the Synscan app, the two star alignment lets you start with the tube in any location, then manually slew to the first star. With a 3 star alignment, you need the tube level and pointed north when you turn the mount on, as the scope will automatically slew to the first star under the assumption the tube was level/facing north. There were some very dicey moments trying a 3 star alignment before I discovered this, as the scope started to slew wildly all over the place, but now I only use the 2 star procedure anyway to avoid stuffing about with leveling the scope and getting an accurate north position.
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