Because corediff needs the relative path (to the platform root), it should check for each scanpath what the platform root should be.
Could add this
cmsPaths = map[string]string{
"/app/etc/local.xml": "magento1",
"/app/etc/env.php": "magento2",
"/wp-config.php": "wordpress",
"/lib/internal/Magento": "magento2",
"/app/design/frontend/Magento": "magento1",
}