If the RAActivator is enabled it'll pick up .rar deployments, and apply a default activation policy to them. So if you want to deploy a -ra.xml file with the activation you will have to do the above.
In IronJacamar 1.1.0.Beta1+ you can do
@org.jboss.jca.embedded.arquillian.Configuration(autoActivate = false)
in your Arquillian based test cases.