I feel like Elena is something of an outlier in terms of D's independent sexual growth because, as D's best friend, she has the same level of trust in her that she does F and so doesn't see her sexual advances as anything sinister or manipulative but as an act of acceptable intimacy between two people who are close with each other. In this context, I couldn't see D doing anything with Martin, or Graham, or Ryan on her own because that level of trust and connection isn't there with them and is why she would need the approval and assurance of F before doing anything with them.
Elena isn't a special case any more than the MC in that regard. She's not an outlier, but a direct influence on D, depending on how far D has been willing to go with her. D can also choose whether to try certain experiences with the MC, as well. And various secondary characters.
Regardless of the mechanics how these choices are made, when it comes to advancing D's part of the story, her personal + sexual growth continue to advance. The only options given to the player are how kinky and multi-partner-based those growth paths might become, I assert.
For example, in the wide-open path, D quite clearly wrestled early with her own attraction to Martin in her home. But, her relationship was already bound to the MC and they had spoken of not doing anything with others without communication and agreement. In that context, she's hasn't tried cheating on the MC. But, she has been fantasizing.
And she cheated with Elena, then owned up to it. Unike the MC's paths, she isn't given the options to cheat with many secondary characters. Really, the MC in this game can be a complete, two-faced jerk if you play the game that way: D, on the other hand, continues to trust in their relationship's integrity even as she grows.
To that point, there was much discussion early on that this game should also enable D the options to do what she wanted without MC's approval, perhaps even in response to learning of his cheating ways. It would be an interesting opportunity to fall apart and later come back together again. But, there is a very loud contingent saying NO NTR and such, so not in the cards. As if the MC's cheating wasn't NTR already ...
I'm not sure I know of any moment where D has the option to try something new with another person and you aren't given that option in the game to explore that path, though - by this point, the player is able to offer D a wealth of choices within the context of sharing experiences with her MC fiance - many of which are proposed or led by the actions we see her initiate in this VN.
You are again trying to make it D's story and all about D. Any choices we have been allowed to make as others were when F was not there for story reasons. Though I understand that wish to make it D's story since she is the thing most players focus on, SHE is actually not the focus of the story, but the Father is. That has nothing to do with game mechanics, but is the base setup of the game. It is about fathers interactions with the world and how that shapes the characters in that world. The one exception to that might actually indeed be Elena, who has some shaping actions on D as well independent of the father, but they are still in his interest more or less.
I believe you continue to get hung up on game mechanics, even though you say otherwise: using the MC as the lever for moving the story to different optional paths is merely a mechanism chosen by the Dev for running this Ren'Py-platform game.
As the player, you are moving a Virtual Novel forward - inherent therein is the notion that the novel has predestined paths (in this case, MC and D as a couple) and then optional paths. Your choices as a player decide how many optional paths occur.
In that regard, MC and D are some major characters - this is not focused on the MC's story alone. They are necessarily a pair from practically the beginning and their dynamic is now to the point where D initiates actions/choices to take as much as the MC.
Do we see scenes where D makes decisions devoid of the MC? Absolutely. Does D offer new ideas that the MC hasn't considered or discussed, especially in Chapter 3 as her character becomes more independent and driven? All of the time. Do other characters have their own subplots and motivations? Since the first Chapter, but increasingly so. And so on - this isn't a story about the MC viewing the world, many tales have an initial lens through which the full storyline and all its paths are made available, but then become far greater than the focus of that lens.
Although this game offers MC and D as the primary characters, coincidentally reflecting the title's hinting at their pairing. The MC grows beyond his prior submission to his ex-wife's control of their daughter, but in this VN it is D who grows the most: the MC becomes her partner and enabler, at best. They both grow in affection to each other and the MC can also be argued as manipulating D towards his affections, but ultimately you are given different levers in which to drive the story and D is certainly the most significant member of it, with MC besides her. It doesn't matter than many choices seem made as the MC, but let's not forget that many choices in Chapter 3 are of mutual agreement - not merely the MC forcing the choice of, say, oral sex or a threesome, whether to agree with secondary character propositions, etc.
