At this point I would not be surprised. If that's the correct intention then it's also showing me Zack deserves the flower way more than Cloud.
And again why is her farewell all about this guy? Is my main thought here if that's the case.
I'm going to be honest with you, I can't think of any take in this story, including a Clerith one, where my main thought isn't "why the hell is her farewell all about this guy".
In fact, I'd argue that this is one of the reason this version is better, because if it's a rejection then it's NOT about Cloud. The thing is that I don't think the refusal of the flower is a conscious rejection by Cloud, who sees the flower and conciously thinks "that would make her my lover, I must reject her". This entire world feels like it exists as a construct of the sub-conscious, the rejection is more symbolic. And the the thing with a symbolic rejection is that it implies that there is something wrong about Cloud and Aerith, something that doesn't fit, they're not right for each other.
And that means that this entire thing is NOT about Cloud, it's about Aerith, it's about Aerith and her feelings and getting them sorted and Cloud is essentially just helping her sort those things out.
Meanwhile, if this WAS romantic, then I have to throw up a bit and call bullshit.
That would make me think "ok, so Aerith dated Zack for over a year, pined over him for 5 years, wears pink for him, wears the bow he gave her, wrote him 89 letters, and became interested in Cloud because of he reminded her of Zack. Then while on a journey with Cloud she confirms that she still likes Zack, and after that her and Cloud split up, then Cloud spends the evening taking care of Tifa and almost kissing her, next day they leave for Cosmo Canyon where Cloud potentially yells at her (all playthroughs should be valid) and she connects with Zack spiritually in the cave of the GI. Then they leave for Nibelheim where Cloud first talks about how simping over Tifa is "totally his thing", after which they split up AGAIN. Then after getting back together they go to the Golden saucer where Tifa tells Aerith about Cloud remembering Zack, which inspires Aerith to write a song about wanting to meet people again, she sees Tifa and Cloud on a date, maybe see them hold hands while she's singing her song assuming she's kinda aware of his presence, she also presumably spends some time with a Tifa who seems strangely giddy. Then they all go to the temple of the ancients where THEY SPLIT UP AGAIN! After which Cloud acts like a psycho, tells her to Hurry the fuck up after the trials, he kills some people and finally tries to steal the black materia from her....... ok, lets pretend for a second that I accept the ludicrous notion that these events were so endearing that it made Aerith fall in love with him, HOW THE HELL is it that this crush is enough to justify making her final farewell all about Cloud?"
Nah, in that case I prefer the farewell to be about Aerith with Cloud being symbolic, mixed with a sense of her feeling like Cloud is someone in need of care or something. But if this were to be truly romantic then...well, I don't think I've ever come across writing this bad.