I ran into a issue with my war using Weld. So i tried to reproduce the issue with tests-arquillian.
But all the deployements are "FlatDeployment". So there is only one BeanDeployment object. Which is not the case with servlet and se bootstraping. So i didn't manage to reproduce my issue (due to multiple ModuleEnablement).
Maybe i completly wrong, but if it's the case it can hide multiple issues...