Well for one, the eroge parts were added because at the time, many Visual novels then had those scenes, so the publisher at the time thought the game wouldn't sell without them, so they were forced in. After it became clear that the people who bought it didn't care about them, they were removed in future re-releases. The Switch version is based on the Vita version, so it won't have those scenes.
Second, if Bayonetta, who's game not only had near-nudity and provocative sexuality but also outright fatalities and torture, can get in Smash Bros, I don't see why Fate/Stay Night should be blacklisted for less.