I think people are missing the fact that most fanmade content that Valve has historically been ok with is all original material. Black Mesa, Portal Stories, and others all used the Valve IP but were all original content. This port actually uses Valve-created content so, regardless of Nintendo’s involvement (although it makes the demand for this action stronger), they legally have to enforce it or risk losing the legal protections for that property.
Nintendo just gave them a convenient way to stop it before they needed to do it anyways.