The main issue is that Electron creates a .desktop shortcut to the app in Linux with the icon set as per default - only the app name. In Linux world this means the app icon needs to be present in the /usr/share/icons folder, or in the app root folder using the name of the app and .png or .svg (png works well and size does not matter)
There are two solutions here:
Copy your app icon to the root folder of your app and rename to <your-app-name>.png
Edit the /usr/share/applications/<your-app-name>.desktop file and change the Icon= to the full path to your app icon in the installed version of your app. Something like: /opt/<your-app-name>/resources/app/build/icon.png
You can also add these solutions to your package.json linux afterInstall .tpl script file.
You might need to logout and login again to view icon changes in desktop.