I've been thinking about this and even talked a bit on the server, but I do think the extra ending could have worked... if it focused on attacking Wayne instead of Reese.
Okay so, neither Wayne nor Reese are particularly affected by mundane physical violence, so I get attacking Wayne instead of Reese, at least at first glance, may look like we're exchanging six for half a dozen. However! One thing you can notice about Wayne is that it's not really that hard to take advantage of his constant overconfidence. In Episode 2, if you have Powerful Build + Street Smart, for example, you are not able to defeat him physically, but you are able to outwit him by pulling his veil off, making him back off immediately; in Episode 3, he claims the Resonant's powers are all "smoke and mirrors", and yet said smoke and mirrors still manage to get him lost until the very end of almost every act of Charlie's "play"; in Episode 4, he mocks Reese for trying to stop him and is immediately glued in place by his Smears, and shortly after that he gets clawed by Reese himself, which clearly affected him more than he lets out. Wayne, at least until this point in the story, is more bark than bite, and is easily knocked off his high horse by things he doesn't take seriously... like, say, a Powerful Build MC bent on antagonizing him.
So how would this "new" ending work? Well, fuck that "wounded pride" comment; make MC take the axe to Wayne repeatedly, doesn't matter if it doesn't land the hit, just swing that shit at him - until Reese takes advantage of Wayne being distracted by MC and throws him out of the window. Simple as that. What happens after that? Well, regardless of the logic behind these actions (maybe you want to help Reese, maybe you really hate Wayne; maybe both), Reese interprets it as MC siding with him and proceeds to leave them there so he can kill Doc, which MC does not witness.
Now, I know this sounds like Obedience route with extra steps, and it kinda is, but I still think it can work in an interest way. Like, you know how Reese gets more forceful and domineering towards MC if you go Matricide/Obedience? This ending could actually mitigate this behavior and make him respect MC more, seeing them like an actual partner in crime and not someone fragile that should be protected at the cost of their agency, while still maintaining the unhinged mindset Reese gets in these routes.
This also could considerably change MC's disposition towards Wayne. After witnessing him being "defeated", it would open a chance for MC to tease and mock Wayne for his loss. I don't know how Wayne himself would react to this, but considering he usually treats an aggressive MC like a child throwing a tantrum, maybe it wouldn't affect him much. Maybe. But part of his mysticism is certainly gone, and Powerful Build, high on hubris, could often advise MC to ignore whatever Wayne says because he's a loser and losers don't get to tell you what to do, right? Besides that, it plays on the thematic of Wayne being an insidious danger because he isolates MC from other people, but now they see he can be dealt with if they have The Power of Friendship(™) by their side (... or they can just ignore all that and think they can totally can deal with Wayne alone now, and proceed to get their ass handled to them. The name is Powerful Build, not Powerful Mind 🤷🏻♀️).
But yeah, these are my thoughts. I just think it's more interesting than "yet another option to ruin Reese's life", you know?