ArvitZ:
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To my understanding the main problem is that both of these tools mainly look at alignment of the telescope tube with respect to the mirrors. But I have to face the reality that at least for my GSO telescope the tube is NOT perfectly aligned with the optical axis of my main mirror.
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Kassar:
This is an issue with which I have to contend. I don't have a permanent observatory, and so I need to adjust my alignment every time I set up my equipment. The GSO tube is not aligned with the secondary mirror holder. I've been considering how I might modify the holder so that I can move it in the transverse directions (call them the x,y directions, where the longitudinal optical axis is the z direction). Nothing has come to mind as of yet, but it seems to me GSO could provide this.
I have a tip-tilt adapter in the path that (mostly) compensates for this misalignment. My very first step is to use a laser to make sure the spot lands on the center of the circle on the secondary mirror. I have a rotator, and so I do my best to make sure the alignment holds through rotation.
I then follow the steps to align the secondary using the alignment scope (I have accumulated several of these over the years). Usually, the tip-tilt does not require iterative adjustment in tandem with the secondary mirror adjustment. Next I follow the instructions for secondary mirror alignment looking at the reflections of the spider vanes.
Last, I do star tests, and usually the aforementioned collimation is satisfactory, not requiring additional adjustments. Prior to performing the first step with the tip-tilt, however, I had noticeable issues with the star test.
Ben