Yes, the output will be used/printed separately but should align. I suppose I can cut the output from a single page export myself, but I would have thought this would be a part of the atlas. It seems like from documentation I should be able to place my own extents that I’ve calculated, which is also not working.
I would also ask, is this part of using the atlas? Or could this be something I am not familiar with how mapping crs to flat output files slightly distort things?