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The main PHD2 PA tool uses drift alignment.
You don't need to align the guidescope to the axis of rotation. Even the new Static PA tool (which requires the SCP to be visible) does not require that as it can calculate it from the movement of the guide star as the mount is rotated.
When you say you can't see the star at the SCP I assume its due to trees or buildings. If its just because they are faint to the naked eye that's not a problem for a camera.
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