I feel like we were supposed to get more out of this VN but something went wrong during development.
Yep. Not a rare occurence i suspect. Most games end up more or less straying away from what their devs first envisioned. It is what it is.
This makes me think that we were supposed to get a Madame Venom without the grotesque futa dong.
I don't think so. Her futa transformation is integral to both her character arc and the way she interacts with other girls. No penis growth would mean no Venom on Lotion/Charger rape, and no Masked Nympho reverse rape. These character dynamics do not feel like a last minute addition to me. As much i would have liked it otherwise, i've no doubt that Madam Venom was conceived as a futa from the start.
It's not Butcha-u first rodeo with dickgirls either. He likes to sprickle them here and there whenever he feels like it.