Indeed, it is very appealing of Yunlan to be so smart and competent! No wonder Shen Wei was interested.

But I think he's also just not a naturally kind person (or a person who values kindness), and his lack of understanding of Zhao Yunlan has a tinge of "not wanting to try" (maybe because he feels he shouldn't have to); I can believe Zhao Yunlan was a monster teenager and nothing would have made that work, but now that he's an adult, some of the things Zhao Xinci doesn't understand about his son, like his loyalty to the SID, are really not that hard to parse.
Zhao Xinci is a bit "look, I'm halping!" about it all, yes. I suspect he's done the parental thing of not updating his mental model of Yunlan past the age he was when he moved out, too. And their moral bases are different enough that Zhao Xinci might truly be unable to see where Yunlan is coming from in some things, irrespective of the trying.