You can only verify tokens in the emulator itself, and not outside the emulator when created in the emulator. See here. Apparently this is for security reasons.
However, it seems they may have updated it in Node v.9.5.0 to work, so you may need to keep reading that support issue.
Otherwise, do not use firebase auth emulator, use regular firebase auth. You can pick and choose which items in the emulator you want to use.
This has nothing to do with JWKURL in and of itself, just the verification of the id token.
J