You can export 2 PNGs one with grid to put GCPs on, and second PNG without grid, but exactly same size (in pixels). And use GCPs put on first grid-equipped PNG to georeference second "grid-free" PNG.
Grid is used only to get pixel coordinates. Dealing with pdf and 'reverse engineering' for me seems a bit complicated stuff, since in addition to 6 georeference parameters, you need to deal with scale and so on, so I'd rather used quick and dirty solution with grid and rasters.
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