ain't no way anyone thought that
That said, I wouldn't call it a yuri rival subplot. She never thought herself competing, and was actually playing shipper-on-deck from the minute she found out Futaba and Takeda were co-workers and that there were the makings of a relationship between them. In fact, her having a childhood crush on Futaba didn't seem like it was initially intended.
I think there are people who were legitimately mad because the only other option is a shota character and they tried to believe the yuri subplot was going somewhere as a cope for that. They're ignoring the fact that Futaba is a loli character because she's "legal on paper" due to her canon age and decided that it was the more "moral and correct" thing to support than her growing out of her thing with Futaba and maturing together with Yuuto. I can't really blame them, but this is a Japanese author we're talking about so you should've expected how some things would turn out coming in.
And yes, the fact that she was supportive of Futaba and Takeda from the start implies she knows she's only hurting herself and Futaba by proxy if she prioritizes keeping everything the same between them. I think the author also mentioned they didn't originally intend for the plot to go this way but went all in when it was decided. CMIIW, but I think Natsumi's first appearance in the anime had the green nail polish, and her first appearance in the manga didn't.
I came to think this is still a type of the aforementioned, but in a slightly less straightforward manner: it's Natsumi's observations of Yuuto's earnestness and selflessness with her in their relationship, that helps her definitively put out this torch she's been carrying in vain as she moves to wholeheartedly support her friend in her romantic endeavor.
...and, possibly, it's supposed to thematically enable her to develop her relationship (whatever that's supposed to be, or will be) with Yuuto in earnest, because now she's matured and can now at least be equals-in-mind with Yuuto (an irony, considering she's several years older than him but this torch carrying stunted her in a way that made her remark that he was more mature than her)? I have the feeling that's what the mangaka is angling towards, but I'm not readily committing to it because-- on top of being unsure if the mangaka intends that-- I'm unsure if the mangaka is that intentional.
No, I think this was intended by the author. The unrequited feelings on Natsumi's part were obvious, but the fact that she never discloses them and noticing Yuuto's efforts and growing maturity implies she's also suffocated by her feelings for Futaba and wants both Futaba and her to live more freely by letting go of the past. Natsumi cares about Futaba a lot, and she's afraid of creating a toxic codependency between them because as we've seen in the flashbacks, Futaba relied on Natsumi a lot when they were in school and Natsumi was probably the only friend she regularly hung around with.
Natsumi feels like her feelings would put Futaba in a cage if she ever disclosed them and they both would revert to old habits. She was afraid her interactions with Yuuto would also put him in a similar state of arrested development, but with the recent chapters with Yuuto becoming more emotionally understanding, even hinting when she fell asleep in his lap that he actually knows she has complex feelings for Futaba (and still wants to be there for her regardless of how their relationship will develop), she's starting to forgive herself for what she considers are selfish actions.
Although, we still can't really ignore the fact that Yuuto is a high school student, but I think it's intentional by the author to show a contrast between how Natsumi and Yuuto's emotional maturity is the opposite of their physical maturity.
Or maybe the author's just a pervert. What do I know.
Maybe confessing is too strong a word for what I had in mind. Natsumi is the type of character I could see disclosing her remnant feelings for Futaba to her in a passive voice or post hoc manner while they were hanging out just to get it off her chest and then reassure her that they're relationship won't ever change. Alternatively, she could disclose it in confidence to Yuuto who is still in her friend-zone at the moment
(also the only character who suspects this chemistry between them from a previous chapter).
She has been in love with her since their school days and now they are in their 20s, so I don't know if she can
will those desires away as appears on the surface to have occurred. It just doesn't seem healthy for her to bottle up and sink those feelings without some outlet with which to acknowledge them. Of course maybe I'm just over-analyzing and not giving Yuuto enough credit.
It might be you're not giving Yuuto enough credit, but I think it's more an example of how adulthood means you have to learn to willingly let go of things you can't control. While it's true that she's had these feelings for Futaba for a long time, she's aware of how detrimental it is for both of them if she keeps dwelling on it when Futaba already has her heart set on Takeda. And as shown in the flashbacks, even back then it's clear she didn't exactly have a chance with Futaba to begin with or even want to pursue anything out of their relationship.
Even intense emotions like love, grief, and grudges, can dissipate if you stop giving it power by keeping them in your mind. Adulthood and emotional maturity are big recurring themes in Natsumi's story arc, and I think the author is trying to show that despite being a flirty busty onee-san, her heart and mind never left high school, which she needs to overcome to finally be free and happy.