Patch already updated on openrepos. But I didn't add the transparent icon, just added option to hide number on folder icon.

If you want to try, replace for example this folder icon:
to your custom-transparent icon with same name and check how it work for you.

P.S. For replace, first remove this icon from phone and after this copy new one to phone. It will give enough time to lipstick understand that icon changed and you don't need restart lipstick.