Having the beans.xml take precedence (option 3 in https://issues.jboss.org/browse/CDI-490) allows you to change the order (or any other configuration) from the descriptor without changing the code.

As an example, if you needed to change something, but didn't have access to the entire build chain to recompile the changes, you would be stuck. However, if the beans.xml took precedence, then you could add your changes to the beans.xml file, allowing you to override the annotations in the code and make your required changes.

GlassFish and other parts of the spec already follow a similar process: https://docs.oracle.com/cd/E19798-01/821-1750/gihzc/index.html

Also, as Martin Kouba stated in CDI-490, this conflict should be logged.