Microprofile has some spec tests that rely on throwing exceptions on deployment. https://github.com/eclipse/microprofile-jwt-auth/blob/master/tck/src/test/java/org/eclipse/microprofile/jwt/tck/container/jaxrs/AppScopedTest.java#L45 is one such test (ignore that it doesn't extend Arquillian).
The problem is that its not the code in the package that generates the exception, but classes added via an ArchiveProcessor, e.g. a CDI extension, that will generate the exception.
I'm not sure the reasoning behind this behavior, but I don't see why ShouldThrowException implies that an archive is not testable. Can this behavior be changed?