Automator quarantine Gatekeeper workaround?
Signature Check

Check your Automator application is being signed correctly. Do this using the command line tool codesign. Use the following command in Terminal.app to view the code signature associated with your application:

codesign -d -vvvv /Applications/MyGreatAutomator.app


Does the output mention your developer identifier? If not, revisit how you sign your application as it may be broken.

Quarantine Flag

The quarantine flag is applied to files downloaded from the Internet. This flag can be manually removed using this command:

xattr -r -d com.apple.quarantine /Applications/MyGreatAutomator.app