Export "packed" without "merge duplicates"

I have a bunch of layered sprite sheets that I would like to export to a fixed PoT size (e.g. 512 x 512). It seems the only way to do this is with the “packed” setting. However, this option doesn’t allow us to uncheck “merge duplicates.” Each of my sprites has to be in the same spot in the sheet for the layering to work in my game regardless of whether or not it’s a duplicate or empty. Any ideas? Thanks!

I have the same problem, I had to do it manually, sucks tho