Not sure I understand exactly what you mean by batch printing, but I do all my final placement adjustments on the bed of the Glowforge directly under the camera, not in Illustrator.
In the particular case of the sheet of cats that I cut out, I had a print file with the cat line art, which I printed on cardstock using my laser printer. Then I had a cut file with just the outlines, where the location of each outline matched the location of the corresponding cat in the print file. I put the printed art on the bed of the GF, centered under the camera and as level as possible (an L shaped ruler helps with this). I pull the cutfile into the GF design software and align over the print as closely as possible. Then I zoom in to the image closest to the camera lens to a level of 450% and fine tune the alignment until it looks perfect. Then I apply the number of clicks previously determined from the graph paper experiment (in my case 2 clicks to the left and 3 up using the arrow keys). Then send the file to the GF, and I usually get very good results.
With my machine I’ve found that if I get the alignment right in the center, it is also good at the edges of my design–although I’ve only tested on a letter sized piece of card stock. YMMV. Also, once the offset is determined, it is consistent day after day, I’ve only updated it once in about 4 months.
Any questions, just holler!