Because you are a pirate.

Yeah but it would be nice to get a heads up on that when selecting the scenario instead of just discovering it halfway through a playthrough when you're wondering why your empire relations didn't change after completing the difficult quest they gave you.

This honestly needs a patch. I found how to write one of my own but the base mod either needs to be explicit about the scenario when selecting it or the faction relations needs to be patched.

The more likely reason this is happening is that the new faction ID wasn't added tot he empire exceptions list in the mod, as writing a patch that does that seems to correct it.