Good call on these two. There's at least one more, but I think you will not be looking in that direction (at least not yet) if you are looking for explicit indicators rather than just subtle hints.
As for Carol and Yuki, you can continue to doubt if you want, but I've had explicit conversations with the Dev about it. That one has been intended from early days. Now, we COULD be dealing with mis-use of vocabulary here. "Threesome" might not be the best word as it suggests a one-off group sex interaction where what I'm expecting is more of a full-fledged "triad" relationship option. If it's not your thing though, I don't think it will be forced on you.
There are themes in this game (which are probably indicators of what the Dev particularly likes.) One is the oft-commented on similarity of physical type of many of the girls. Another is D/s play in a couple of different configurations. Footplay is a very common option placed before us, as well as anal. I think all of these are probably pretty obvious to any but the most casual player by this point. Well, I think the triad relationship configuration is another which just hasn't been fully fleshed out yet because Dev is solidifying the one-on-one relationships first.
As always, time will prove.