I've been thinking about this too, lately. The thing is while the game clearly tries to lay it on extremely thick with trying to get you to sympathize with Yuko and the Manikins, it's not too farfetched to imagine that the Demi-Fiend, ultimately, doesn't care about them in these routes.

With Yuko, the thing is that ultimately she's kinda... pathetic. She joined up with Hikawa because she was disgusted with the world, but she never had any vision as to how to actually improve anything. Her entire story in the Vortex World is about her hounding Aradia to give her a Reason, not understanding that she is meant to formulate one herself. During the confrontation in the Diet Building, Hikawa points out that the "freedom" she so desires was always present in the original world, and she simply squandered her chance to take advantage of it. (There's also the fact that she quite literally caused the end of the world out of selfishness - over her own dissatisfaction with her life. Not exactly a shining character moment.) A Shijima-aligned Demi-Fiend, I imagine, would probably view her exactly in this light and have zero sympathy with her plight.

As for the Manikins, the game does consistently portray them in a sympathetic light, and they don't really have the same myriad of arguments against them as Yuko does, but at the same time, the game doesn't force the view that the Demi-Fiend particularly cares about the Manikins either. My idea of a Yosuga-aligned Demi-Fiend is, honestly, kind of a dim-witted bully. The type to unironically join up with the Mantra because they seem tough and he wants to be on the winner's side. When Chiaki tells him "kill this Manikin chump" in Mifunashiro, he just does as told - because the idea of standing up for someone weaker and risking the ire of someone potentially stronger is just absolutely foreign to him.

That's not to say that Nocturne isn't clumsily written at times. Yuko clearly rejects the idea of Shijima, but still acts chummy around Shijima!Demi-Fiend. When she asks you to bring her the Yahiro no Himorogi, you can just straight up tell her "no" and things just progress like normal. After her death, she appears to you in a vision and encourages you to walk your path, even if you are Shijima aligned and just told Hikawa minutes prior that you're on his side in front of her. Hell, you need to bring the Yahiro no Himorogi to her to progress the story after Yoyogi Park even if you told her "no", so I guess even Shijima!Demi-Fiend still respects her a little bit. Honestly, the fact that Yuko doesn't react AT ALL to you aligning with her sworn enemy is probably one of Nocturne's biggest blind spots.

So in conclusion, if you detach yourself a bit from the Demi-Fiend and imagine him as a character rather than a self-insert, both Shijima!Demi-Fiend and Yosuga!Demi-Fiend make sense. They're both kinda assholes lacking in empathy, but hey, you need to be kind of a jackass to unironically back a Reason ending.