Not showing in Spotlight

[ghost]

The app does not show in Spotlight search.

Maybe that's the issue with NSPrincipalClass from the plist?

From the docs:

NSPrincipalClass (String - macOS). This key contains a string with the name of a bundle’s principal class. This key is used to identify the entry point for dynamically loaded code, such as plug-ins and other dynamically-loaded bundles. The principal class of a bundle typically controls all other classes in the bundle and mediates between those classes and any classes outside the bundle. The class identified by this value can be retrieved using the principalClass method of NSBundle. For Cocoa apps, the value for this key is NSApplication by default.

Yours has AtomApplication which is not even mentioned.