I repeatedly get this problem for an app I'm developing Xcode (yes, the app is signed with a developer certificate). The message keeps appearing every few minutes to every few seconds. Even after a reboot, I'm greeted by this message. It has killed the user experience.
At the very least, this alert should have a checkbox for "don't show me this again for this app – ever".
Yes, yes, I know: file a feedback. But, I've completely lost faith in the feedback system when it comes to getting problems fixed with macOS. The last few major issues I've run into, I've had to file a DTS request to get them to look at it and confirm the bug to finally get attention for a feedback filing.