Any news?
Just stumbled across this thread as I also need a solution for merging layers on export. Is there any solution for this? Thanks!
Just tried fixing the plug-in above. I can get it to be called in Glyphs 3 on export but it seems what the plug-in can access is practically sanitized. The layer’s parent (the glyph) has all other layers removed, and all additional masters in the font are removed as well.
What can I do? I think this is a reasonable request.
I am still waiting for this to work for Glyphs 3 four years later 
Would be awesome!
Here is a new plugin that does what Georg’s plugin does plus a little bit more.
There is a tutorial in the readme, but very shortly: You go to Filters > Combine Layers and create your combination, which entails choosing the layer(s) you want to add on top of the current master, and you choose the boolean (add, exclude, intersection) and direction (current direction, opposite direction, all positive, all negative) of selected layer. It makes the export instance for you with the proper custom parameters. You can also just make custom parameters, e g Filter = CombineLayers;Cutout;exclusion;positive
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