The moral of the story technically for the lore of this NTR game, is that the girls were waiting & wanting the men of their choice (which are of course, Ken, and the Priest guy forget his name, father Thomas I think? anyways I digress), to be bold and perved on by Ken & the priest guy. The girls didn't want the old man to be the one who's forward in perving all over them, but the girls settled for the Mayor because he was the only one making the moves showing an interest to do dirty things with them.
I would argue that if there was ever an actual third ending, most people forgot about this, but in the beginning Ken was going to tell Millie that he loved her, but ended up stating that he thought of her like a sister/ sibling instead fearing that she probably wouldn't feel the same but in fact push/ distance herself away from him, so he called her a sister rather than a lover. So if I were to guess, the third ending probably would've concluded with Ken confessing to Millie much earlier, but in all honesty I would suspect that there might still be NTR because Ken seems to act like he doesn't have a libido to act on impure thoughts to perv all over Millie like she wanted, she would've just been NTR'd by the mayor anyways even if they got married.