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You seem to assume Toady is autistic, or egoistical, or oblivious of the world around him. Just because he's independent from big gaming companies or teams doesn't mean he doesn't have to rely on his community, far from it. I don't just mean bay12, I actually mean the community of all people who could potentially play his game, which includes the indie community (where he's acquired quite a bit of notoriety as the numerous conventions he's been invited to can testify) and the gaming community in general. A community isn't a fixed set of people: some quit playing after a while, some get introduced and start contributing right away. As older players eventually move on and leave, newer players have to join so the community doesn't just die like it happened to far too many forums with the advent of social media and aggregating websites like Reddit or 4chan. Because the game doesn't advertise itself, these newer players have to be pulled from this "outer community", so to speak, or through word-of-mouth. So yeah, keeping the game attractive and the bay12 community welcoming is crucial to the game if the bay12 team is to keep relying on donations for financial support. That doesn't mean the game has to pander to noobs or anything, far from it! Complex and intricate games have their target audience, and Toady has forged enough of a name for himself that people are willing to support him so he can keep perfecting his masterpiece of game design.
But rape (and the aforementioned things in the thread, such as dividing humans into races) doesn't add anything to the game design. Gruesome combat logs are an emerging consequence of having a detailed body anatomy and step-by-step, formal combat actions. Rape on the other hand would have to stem from a conscious decision from the developer, saying: "I want characters to be raped in this game". Just like "I want homophobia to be a thing in this game" or "I want distinct biological human races to exist in this game". I don't actually think such a move would upset that many people, but there's a substantial risk that it could tick off enough gaming journalists or voices in social media that it'd get some bad publicity, and soon enough the game would be known as "that weird nerd rape fantasy simulator thing", regardless of how minor the change would be. (Let it be known for the record that although I'd find it weird, I wouldn't mind much the existence of such things in the game as long as they're opt-out modwise, but then I haven't been a victim of rape or homophobia so I'm not one to judge.) Worse, if the bad publicity spirals out of control because of some backlash from this community (which is extremely likely as people here are understandably fond of their toad, but also -and less understandably- likely to frequent chans or reddit, and thus have a strong opinion of the so-called 'SJWs' or 'PC crowd'), this will forever taint the game and its players, regardless of the game's merit and regardless of how welcoming the forums have been in the past. Incidentally, this policy of being ever welcoming to outsiders may explain the zero tolerance Toady has for any explicit material or rudeness on his forum. Put it another way, when girls at parties ask you what games you play, you don't want to be replying "yeah it's that game with racist shitting dwarves, also you can craft dildos menacing with spikes and rape elf kids". Or have them think that when they google the game's name.
So yeah, being welcoming to others is paramount to the long term life of the game. It's not about hurting some feelings, it's about turning off swathes of people that could otherwise join the community and support the game. Someone who doesn't feel comfortable playing a sim game with rape doesn't have any hurt feeling, it's just that they'd rather be doing something else in their spare time that doesn't involve rape stories. And to address your argument about how the, let's say, "hardcore fans" would keep the game alive on their own, I have my doubts. Even hardcore fans eventually quit after a while, or can't afford donating forever. Remember a community's never static, and when these dedicated members eventually leave for various reasons, who is going to replace them? Even Trump is starting to realize that alienating entire demographics by capitalizing solely on "angry white males and their wives" can only take you so far. I'm not saying that a hardcore DF fan is a Trump supporter, let's not push the analogy too far. But at the end of the day it's all about demographics, and if your livelihood relies on the support of good-willed people who don't owe you anything, it's always a bad idea to cut onself off a demographic. It doesn't matter whether the reasons for doing so are justified or if said alienation wasn't intentional.
And at last, I don't think Toady has given any hints that he was being censored in his art expression in any way by 'PC' or whatever. Just like I said before, you have to consider the possibility that maybe, even if he was being given millions to do so, he isn't that keen on rape stories or anything like that, just like a significant chunk of the population.