Kind of a late reply, but I wanted to mention that in real-life poly relationships, it's very common for people to continue having dates and sex one-on-one (as a dyad) sometimes the majority (or even all) of the time, even in a non-hierarchal triad like MC, Josy, and Maya have. Honestly, the fact that the MC continues to do some stuff with just Josy or Maya rather than only doing things all together and having constant threesomes makes it more realistic and believable, and makes the times they all do stuff together more special.
I do think your choices of who to do stuff with will influence things though further down the line, as well as some dialogue choices (for example, there's some dialogue choices where you can pick whether to support Josy/Maya relationship or not). In fact, your choices already have had a bit of an impact. After the Halloween party, when Josy and Maya are talking about their sexual experience with you, if things are roughly even, you get points with both of them, but if you've favored one of them over the other, the other losses points. Dealing with jealousy is a real potential challenge in poly relationships, so it wouldn't surprise me if there's some in-game reflection of that and these decisions become more impactful later on regarding if the triad survives or not.
Also, I think Josy and Maya being a little scared of adding the MC to their relationship is a perfectly justified feeling as well since it's introducing a huge new variable that, if it goes poorly, could severely damage their existing relationship. Frankly, those type of concerns are normal for a big change and the fact they are talking openly about them bodes well.
Lastly, the walkthrough is designed to avoid spoilers as much as possible. Referring to them as a throuple would be a spoiler. In-game, it's not surprising they haven't called themselves a throuple either since 1) they've only really recently started defining their relationship, 2) they aren't public about all being with each other, and 3) if they were to describe their relationship to someone, "the three of us are in a relationship together" is going to be more easily understood by most people than using poly terminology.