transfer pavilion to table should not involve your machine at all. The transfer and its alignment is 100% in your transfer fixture and its use. If you experience a shift the first question to ask, is the dop keyed or not. If dops keyed are both matching and machined the same if not keyed it is on your extra alignment methods before locking into the quill axis. One can and many do easily transfer a keyed dop with a stone to a round dop for table facets, it just takes more work and possibly tools to adjust the alignment after the transfer back to 100% alignment with the quill axis.
i teach faceting. if you are now cutting the top, DO NOT cut strait down to girdle. cut a small ways, then cut the girdle row of facets going around matching the new one to one just cut and when you get all the way around you can see if it matches and if not which way you need to adjust the horizontal cheater to recut a little more till you get a good match, then cut down to girdle area. email@example.com