so if I understand it correctly, you are running only tests in SE, so you must be using Weld SE for that. I'm not sure I can see the structure you have in place (the "subproject"), but first thing coming to mind is using a synthetic archive for testing - e.g. disabling discovery for Weld SE and telling Weld what exactly you want to have in the archive. Note that this disregards beans.xml you have there and based on your structure this may or may nor be a problem to put together; worth a shot though.
As for how to do it, take a look here, namely the snippet which does disableDiscovery().
If you were running tests in EE, then Arquillian is the answer as you can, via Shrinkwrap, decide what will be in the deployed archive hence leave out any unwanted bits.
Also, what is the reason to avoid having those beans in place? From what you say it doesn't like they are alternatives you want to replace? Weld is lazy and won't actually create those beans unless you try to use them in your tests. Obviously, it will still discover them and validate them, but that's about all that happens.