Native bundled apps for OS X generated by javafxpackager can't be signed by codesign. This is because they have a symlink in the JRE to libjli.dylib.

Signing for the app store is different than Gatekeeper compatibility because you have to sign all binaries in the application bundle. When encounters a symlink it will replace the symlink with the original file after signing the binary, and will cause the app will stop working because the loader path for libjlib.dylib needs to find all dependent libraries in the same directory.