Warnings - the final frontier

I have a story up on AO3 with a "rape/non-con" archive warning. Today, I received a (very polite and not at all flamey!) comment remarking that the rape was difficult to read, and that a trigger warning might have been a good idea.

Incidentally, I also thought that a trigger warning would be a good idea for this story. That's why I used the archive warning.

Now I'm wondering - did the reader overlook the warning, or did she feel there should have been another warning within the text itself to mark the passages in question? I suspect I'm not entirely up to date on the eternal "warnings" discussion.