Pretty much what it says in the title, Carrier appears to be unable to pick up non-vanilla mobs. I don't know if this is a limitation of what's possible, or a bug, or if extending the ability to carry friendly mobs to mods like Earth2Java is possible, but it would be cool to see if possible.

Thanks for your time, and for the mod of course.

You answered the question in the comments for the mod, thanks again!