The wife becoming more assertive during the denial options shouldn't have been a bad end imo. An ending, sure it works, but just dropping it like that and not showing how the new dynamics work just feels like a missed opportunity. It's also really binary, if you give her any control once you're locked into the bad end, there's no middle ground.
Might be wrong on this but I believe the reason it's a "bad end" is cause Zoe is always shown to be the alpha and depending on what you pick. Her plans are either to actually help the married couple (to some degree at least or in her own twisted way), make the wife her slave or just use/exploit the wife but she is always shown to be the "alpha" or the dom.
So her losing control and being "subjugated" would mean that her whole plan backfired or the fact that she was turned from a dom into a sub. Personally I agree that depending on how you look at it, it's not a "bad end" but when Zoe represents sexual prowess losing that part and being put under someone else in a sexual relationship would kinda mean the death/defeat of who she is.
Though this might be mostly speculative on my part. I also agree that the edge path for now is seemingly unfinished and by my guess it will be further developed in the future. Seeing as even if you follow it without getting the bad ending it for now doesn't go anywhere when you finish from what I could find. Like for instance if I check with a saveeditor there are 12 paths listed in the editor. Anal, boot, collar, denial, excluded, hair, orgasm, plug, stop, threesome, vibe and voyeur. So it might be that there are 12 planned paths/endings but only 5 are implemented or fairly finished yet. There are also the mentioned true ending / endings? that might need you to play through a lot of the paths or doing things in a certain order or with certain choices.
Like for instance in some of the paths Zoe has mentioned or at least thought about how she wants the husband as well. Not sure if it's a specific path but at one point Zoe will think that the husband would look great with make up. Or during I believe it was the exhibition or the gangband path Zoe will also think that now that the wife is "done" it might be good to start working on the other one or something (which to me implied she was gonna target the husband next) but at that point the path pretty much ended so there wasn't anything more after that for now.
Seeing as the title is called Building "our" futafuture for now there is only a focus on the wife + futa future but I believe the title is aimed at the our as in husband + wife's futafuture. So there will probably be either a few paths going for the husband as well and probably the true ending of this game will have the husband + wife turn into the sex slaves of the futa.