I had chosen to be the shulk and played for an hour or so. But after leaving the world, changing some server config setting (for FTB Essentials) and re-joining it asked me again to pick an origin. This time I chose the enderian but I kept the shulks benefits as well. Changing using commands works for changing my second origin, but it seems like I always keep the benefits from shulk. When I press 'o' to see my origin it just shows whatever the latest is (e.g. enderian)

Changing to shulk and then something else using commands worked!