When you start converting people to a new species, it creates a second colony on the same planet - that's part of aurora, a colony, programing-wise, can only support 1 species. You have to make sure you have the right one selected when you give the load colonists order.
If you're creating an uninhabbited colony for them to deposit stuff at ahead of time, you need to make sure you have the right species selected and manually create it. Just dropping stuff on a planet iirc auto-creates a colony for your original species.
What do you mean you can't terra mod?
I believe you have to generate the new species on the planet they are to live on.
Only if you're using SM mode to create a new species as a new empire.