There aren't any. I think taking the angle of dissecting the elements of fangames themselves that make them fangames is a fruitless task; as you said, basically every core principle of IWBTG has been neglected by at least one prominent fangame, and the further you carry on abstracting the further you get from IWBTG. If some fangames don't include delicious fruit or spikes as traps then maybe it's just having traps that can kill you in one hit that is a core feature of being a fangame, but then Spelunky has traps that can kill you in one hit and that's definitely not a fangame, etc.
It's not one thing and I don't even think you could broaden it to a set of qualities either - at least not without having criteria that doesn't represent a majority of fangames.
Honestly I'd say that it's not what a fangame entails or features that makes it a fangame so much as it is the online space in which the fangame exists and the way people in that space respond to it. E.g. If Boshy wasn't released into the IWBTG community would it have been necessarily perceived as a fangame? I'm not sure.
It might sound simplistic but fangames are fangames when we say they're fangames and when the community plays them as fangames. I think it ignores too much diversity to attempt to lay out fangame classification rules even on a hypothetical basis.