The only issue with that is my stories almost always contains explicit sexual content, which means I have to use the Explicit rating no matter what. So the rating doesn't help to differentiate between a fluffy fic where sex happens versus a dark fic where sex happens.

Explicit isn't only for sexual content though. It also is for graphic violence and other "adult" themes. I get that in your context, readers may expect it to be explicit sexual content, but can you not make it clear in the story tags and in the description that is not the only thing the E rating is for?

I've seen some authors add to the story description something like "Please read the tags carefully before proceeding with this fic" and have tagged some of the topics you mentioned in the OP. They don't tag each individual chapter.