Specifically, he didn’t understand human, didn’t understand how to communicate with human, didn‘t understand that human treats relationship differently. Just think of Jin clan as different species than human that speaks different language, has different nature, has different social norms and rules. It is easier to understand why he did things in the past.
He maybe killed his father maybe because death means nothing in Jin clan. Jin clan’s people generally didn’t care if friends or colleagues or family died, because they mean nothing. There is no concept of love, family love, or filial relationship among Jin clan. All types of relationship in Jin clan is bound by contract, for example, subordination contract, like master-slave. So maybe he just wanted to make the uke his own and not to thing of anything else, but failed to understand that family love exist.

Sooooooooo...... past emperor was just really, really, REALLY horny (not that he isn't now). And he really did love uke, just didn't know how to communicate?
Any who, so the seme killed his own son bc the uke was giving him too much attention. What doesn't make sense is doing it in the room with the beheaded son.
Cutting off the hand(s) of the uke's best friend bc he tried to help him escape somewhat makes sense in the seme's messed up mind.
But the death of the uke's father makes no sense. That's the one of the things I don't understand. Did the seme really kill him? Why did he hold a funeral for the father, but not let the uke go? And why give the uke some pieces of evidence?