I assume that multiple entries might have been generating because of using the "rename" option - since 7-zip doesn't have an option to specify destination directory when adding files, it is commonly advised to add the files as-is and then move them wherever you want, so I did,
cd resources
7z a ../Editor-Mac.zip app
7z rn ../Editor-Mac.zip app Electron.app/Contents/Resources/app
cd ..
This is given directory structure like
Editor.exe (Windows binary)
Editor-Win.zip
Editor-Mac.zip
resources/
app/ (has the actual changing files)
I'll see if there are better options - my concern about merging a Electron.app directory was that this overwrites file access permissions on it (so it's no longer +x) but having duplicate entries in the archive probably isn't much better.