If subtlety doesn't work, then yes, I would clarify. If I think someone is misinterpreting, I would clarify as well. But I certainly wouldn't interrupt something that is going smoothly as has been done to me.
To be fair, there were other issues with my ex so it was important not to distract me at all when I was in the mood or I would stop being in the mood. Also, it was about phrasing. He would say things like "do you want to make love tonight?" which seemed clumsy at best. If he had said "let's fuck", that would have been less of a turn-off, I think. It would still have seemed weird to state the obvious that way, though.
A female friend of mine once was interested in having sex with a male friend we had in common. She flirted with him a lot and was hoping that one thing would lead to another. Then he suddenly asked in the middle of a flirting session "so, what about a booty call?" and she said it was like a cold shower.
I think in these cases, the problem is that suddenly, you start questioning if the person respects you, will respect you after the sex, is objectifying you, etc. That's what seemed to go through her head and nothing happened between the two of them, which is sad. If he had put his hand on her hip and leaned forward, I'm positive they would have become FWBs.
This being said, once again phrasing might have been in question. If he had told her "you know, I find you really hot, what do you say we go to my place and have some fun?" she probably would have been less shocked and more willing. Of course I can't speak for her.