Here's how I see it. IP holders usually interfere with cases of fair use when there is a direct threat to their own commercial activity, ongoing or planned. For instance, Take Two has taken down project Re3 few months before they released their own remaster simply because it could very well impact its sales - some people could download this project instead and have a decent technical remaster (new engine, better compatibility) for free, shifting their interest from Rockstar's own remaster. I think that every single C&D take down happens for this reason, whether the public is aware of the true reason behind or not.
OpenMW is another possible example - Bethesda forced them to stop the distribution of Android version. I'm not sure when the take down happened exactly, but I think this could happen because of their plans for or actual release of (depending on when it happened) TES: Blades mobile game. I see no other reason why would they demand only the android builds excluded and leave the rest be.
There's a lot of different projects that haven't been taken down, which leads me to the conclusion that this is predominantly tied with whether or not is the project impacting IP holder's activities.
Now, I have no idea whether this might be my case or not. What I chose to believe based on my observations is that Bethesda is not very interested in anything regarding the classic Fallout games. Maybe it's out of respect to the fact that they are not truly their products, maybe it's just because there's not many of us dinosaurs playing these old games to be considered as a significant market they'd really need. Whatever the reason, there's far too many projects and mods based on the classic games that have been around for years, more than a decade even in some cases, very popular among the older fans that must have appeared on Beth's radar and yet haven't been taken down.
We'll see what the future has prepared for us.