Well it's kind of a difficult place to be in because of how RN has been treated. The ideal way for it to work would have been for FSN to have been TL'ed, RN TL'ed, and then someone to have come in and made some kind of fusion patch, but the order was mixed around. MM first added the voices to FSN, then Waku Waku added some but not all of the new effects and scenes from RN, so RN turned into something you patched into FSN because of this. The project started out with Waku Waku putting the MM text into RN, as a more efficient version of the RN patch he did for the 2004 FSN, as it's easier to put FSN into RN than it is to put RN into FSN, so in order to avoid alienating the audiences I wanted to keep the experience of "FSN with RN features" but also provide something else that was just full on RN, but since we had access to the text changes I decided I would apply some, such as the removal of some uses of "x says this in a y tone" since RN is voiced, and the removal of some more infamous moments like some of Shirou's rather sexist comments that have given him a rather negative reputation in the community, but was very conservative towards the FSN version of the text.
To answer your question, other references to Sakura being raped were made into if statments as well, in fact I might just change that because I think I went overboard. I blame UBW for this. In Fate I only added if statments to things like references to the H scenes and whatnot, and left lines like "Kill them or rape them" from Illya to Berserker alone. but then in UBW, there was so little sexual content I kinda became sort of super observant and used them on things I may have overlooked in Fate and HF, such as Shirou feeling Rin's breasts when they were hiding in the corner, or the line about Shinji imagining himself raping Saber. It also doesn't help that the scene where Caster tortures Saber was considered an H scene so I used if statements on those too. So by the time I got to HF, UBW had put me into the mindset of, "if it's sexual, then use an if statement." I think I may have gone overboard as I probably don't need to accomodate the different versions of Sakura's other abuses........no wait......shit I do because of the Lust Worms vs Crest Worms, which is important to the H/H alts.......damn. See, it's tough to find where to draw the line. Though I think some stuff like Kotomine saying she has suffered sexual abuse and Sakura herself saying she was raped while they were in the rain could be left in, so I'll go ahead and change that when I fix the other stuff.
Clarifying the suggestion I made: Basically the uncensoring switch and the H switch are independant of one another so if we use the unensoring switch to keep the original version of the Shinji/Sakura relationship, you can keep H scenes off, leave uncensoring on, which normally would do nothing without H scenes on but in this case would be the new flag check for the Shinji Sakura content.