Isabelle first meets Lynn in rather humiliating circumstances, and the humiliation is deepened when "Lynn" is a man. This puts a distance between them that Eden never really cares to mend. There's a lack of feminine solidarity between them like there is when Eden is Lynn (which is a funny thing to say since Lynn enables Cy so much and Isabelle's not even really a woman, but still) that makes for more distance.

However, Isabelle's own trauma and general nonthreateningness enables Eden to open up to her a bit and share things in one instance that he wouldn't really share with others. It's not enough to form the kind of bond that Isabelle has with Lynn in Nullverse canon, though. When they do have threeway sex with Cy, he's less inclined to go easy on her than Cy is, which contributes to Isabelle's sort of morbid interest in him. She won't pursue it if she's in a good headspace, though.

As for twin!Eden, I don't really know! That AU is new enough that when I discussed it with Null there wasn't enough groundwork to go on. But honestly, I would expect that they'd be pretty distant. Cy likes to keep a small social circle too, so there's also a chance that if he already had two submissives he wouldn't go for a third. Who knows, though? Not me or Null at the moment, that's for sure.