I haven't played chapter 3 yet, but I think the "rape" tag should only be added when there is explicit rape in the game. Whether flashback or not. If rape is only used as a dramatic device or in a character's past but nothing explicit is shown, it shouldn't be added.
For example, Hillside. The game has the rape tag because it shows a scene that happened to a love interest, but the game doesn't use rape as a fetish.
Anyway. I fucking hate rape plots as character backgrounds. The description of the tag doesn't specify its use, but if it's only mentioned and nothing explicit is shown, I don't think the tag should be added.
What is the case here, is it just mentioned or is something mildly explicit shown?