The reason used to be because the prologue established the incest storyline so it was away from Patreon's eyes.
That's not the reason.
The prologue was a first attempt before SLim's abilities improved and it subsequently became outdated. The current build was a remake to reflect SLim's better understanding of Renpy allowing a departure from the more linear branched VN formula in favour of a more free-roaming approach where a big part of the gameplay loop is
finding the content, and his improved artistic abilities with using Daz.
The prologue was simply omitted from the new version because people preferred to get new content first, remaking an updated version of the prologue and integrating it into the current build has always been the plan as far as I'm aware and has featured on priority polls for a long time.
The old prologue builds were on Patreon (incest was an externally available patch) and the current game previously had the ability to continue that incest theme in earlier builds by allowing players to custom input the relationships even on Patreon. Patreon eventually put a stop to the custom input despite it not explicitly being mom or sister etc. as options just because it was possible for players to put those words in.
I can't speak for him but I don't believe SLim ever intended The Awakening to be a straight-up incest game. I think he was inspired by games like Milfy City (which hadn't fallen from anyone's graces yet back then) and just wanted people to have the option. If I remember correctly, around the time Patreon demanded the removal of custom inputs they were also going after SLim for supposedly including underage sex. They clearly hadn't actually checked the game and it seemed like they were going off reports, so it seems likely someone with a stick up their butt or an axe to grind were trying to cause some shit. If that's the case then I'd say they're responsible for it no longer being an option.