What about even simpler solution: each led is separate full size image (same size as overlay), each led file is mainly empty except led image in correct position (relative to original overlay), everything else is transparent, file name is used to find correct led image (df0 led for example would be original-overlay-name_df0.png)
Led off: show main overlay normally.
Led on: any non-transparent part of led image is temporarily copied over main overlay image.
Very simple. No need for annoying coordinate files!
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