What's difference between the alignments created by Geometry best fit and Bore pattern best fit?

[[Ap...]]

Assuming I have 3 planes and the bottom one as primary datum A. The another 2 planes are secondary B and tertiary C. These are theoretically perpendicular to each other. The base alignment is created by A (spatial to Z), B and C.

Now I also have some parallel cylinders perpendicular to datum A. For the following situations, I am wondering what are the differences between the 2 new alignments?

1. Create a "Geometry best fit" which inherited from base alignment. Select all the cylinders for allowing X and Y translation. I can then have a new "geometry best fit" alignment fitted by LSQ.
2. Use "Bore pattern" of the true position, select base alignment first and all the cylinders for best fit, with Gauss method and check the box for translation in X and Y. I can then get a "best fit" alignment which also fitted by LSQ.

Does these 2 use different point data for best fit? or what are the differences?

Thanks.

[[Me...]]

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Method 1= LSQ fitting of all measured points.
Method 2= LSQ fitting of substitute cylinder midpoint's.

[[Ap...]]

Here are the features defined by one of the Zeiss book)
Nominal feature (CAD) - Actual feature (part) - Extracted feature (point cloud) - Associated feature (substitute) .
So when we select the features in Calypso, how do we know which is used?