Nemo Glass's Links
In the "best/good endings," Nemo is grateful that they are able to maintain their friendship with Timothy. During their adventure in Silent Hill, they became friends through trial and fire, and they didn't want to lose that afterwards.
He helped them through parts of their journey, and they reciprocated the gesture. Even if at times that involved some uncomfortable and heavy conversations. They were originally a little sad when they part ways so that he could find his boyfriend in the normal world, but given they needed to face Nikolai, they knew it was probably for the better.
They are grateful that he is willing to be civil with Nikolai as they help guide their old friend into and through non-cult life.
... "Civil" is a relative term, they know, given the pranks, but given what Nikolai had done, they are not going to be mad at deserved behavior.
They know Timothy is still hurting deeply from his own traumas, and they try to offer support as much as they can. Others had helped them out of their problems, and they want to offer the same to him.
In their "good ending", Nemo is something Timothy has not had in a long time: a true platonic connection. They are his close friend, and after everything the two went through in Silent Hill, he trusts them completely-a rare occurrence for someone so beaten down by life. Tim is even willing to put up with Nikolai for their sake, despite the man's attempts at weaponizing his trauma to manipulate Nemo with. He is still stunned and touched by how much they seem to care about him.