app.jar is the archive produced by the bootJar task. This is a Spring Boot fat jar that contains all of the module’s dependencies as well as its classes and resources. It can be run using java -jar.
app-plain.jar is the archive produced by the jar task. This is a plain or standard jar file that contains only the module’s classes and resources.
You can learn a bit more about this in the documentation for Spring Boot’s Gradle plugin.