Khan was young. He had traveled a lot and met many species. The density of his experiences was exceptional. However, he was merely twenty-four years old. Khan couldn't have the wisdom to conceive the universe as a whole, let alone decide its fate.
Khan's recent political move had also separated him from every existing force. He had Baoway, but that was no species. He sort of had the Thilku, but acceptance and belonging were different. His cape wasn't enough to change his flag.
So, the Emperor's concerns were on point. Khan had no reason to fight for the universe. He didn't need to work so hard to defend it. Khan shouldn't even understand what was best for that infinite environment, but there he was, claiming that he would pursue that grand, impossible mission over a handful of affections.