He doesn’t feel at ease, he needs her expertise, just like he needed her to run his country for him while he fucked off and had an affair. His takeaway from being mistreated as the child of a consort wasn’t to be faithful to his wife but rather to not knock up his own consort (who he’s also at times treated like shit!) He was threatened by the competence of his wife and worked her to death while fooling around with his consort. He sucks dude
Your points are valid.
I don't see him as someone threatened by his wife's skill though. In fact, it's more like he's aware of his own incompetence and he knows he can't run the country on his own because he knows he isn't capable. He's a scumbag for what he did to Louise and to his lover and actually, I don't like him one bit. I just think that his mother's schemes and manipulation was what made him into who he is and if not for that, he could have been somewhat decent. Needing Louise's expertise and being at ease with her because he knows she is more skillful than him in both running the country and in personal problem solvings can both coexist and does not necessarily negate each other.
in another life, Louise and the current emperor could have been friends seeing as the emperor feels at ease enough with Louise to deem her be the only one he trusts enough to divulge his secret on. If only his mother isn't such a scheming biatch, he could have grown up to be a decent human being. Welp.