That is a great question and I completely understand where you are coming from. I'm sorry you're dealing with shame around it, that's not an easy thing carry.
To answer your question, in my head, when Qui-Gon and Ani do age play they very rarely do things that would normally be considered sexual because the age play itself is sex in its own right (I don't know if that makes sense, but there's certainly a level of intimacy and sex isn't only penetrative)
I think they've only really had "sex" once during age play and that's in the second chapter of there is no forgiveness without love and they used as a way to rebuild trust. (I feel like there was another time and I just can't remember... was it the cock warming one I'm thinking of?)
So they definitely have had sex while they are playing when Anakin is little. I kind of think of it like they started more with that because it was a little more familiar for the two of them (hence, Qui-Gon and Xan exploring it a little in a much more sexual/humiliation way). As Qui-Gon and Ani grew more comfortable with it, however, then it became much less overtly sexual.
But I don't think either of them see anything wrong with penetrative sex during age play. They just kind of... go with the flow.
As a side note, I guess I personally have a pretty open view of penetrative sex and don't really see it as something that has to be between two people because though that is a way I experience intimacy and connection with my partner, it is far from the only way I experience that. In fact, I probably find sex more as "fun" and I sometimes prefer intimacy in different ways. Now, I completely understand that that is not for everyone, I'm just saying that's how it works for me and I think I definitely have projected that onto this little polycule in Three's Company lol.
I honestly don't see anything wrong with mixing sex and age play and i don't see anything wrong with keeping it separate either. It's just up to what people like and what their fantasies are. There are no bad fantasies, only bad behavior.
I don't know if this helps or answers your question, Anon, but I hope you find some peace with exploring your kink 💗