Eleven didn't mean it quite like that. He meant that the TARDIS would be happy to have another one of him come and visit. Between however many of them were on the Enterprise, he doubted she was ever alone for too long.

"You can't still hear her?" That's what he thought of it as. Hearing her. "She knows we're here I'm sure, and she doesn't take us where we don't need to be."

So following that logic, the ship would also know what would happen to her if they wound up here.