Your assumption that it is Futaba has flaws, 1 is that she hasn't reappeared since that flashback and even before then she hadn't been there since the watch was given over. There might have been one more appearance that I forgot but this is all many chapters ago meaning it would be a terrible Checkov's gun regardless. Checkov's gun only works if you remind the audience it's there.
If by "that flashback" you're referring to Yotsuha's flashback of her journey thus far, then please see below for Fuu-chan's appearances following Ch 43
Ch 49
Ch 61
The 2nd problem is that we don't know what motives there are. Almost everyone assumes time travel is involved but there is no proof either way that clover is a time traveller. There isn't even any proof that there is a motive that people would accept as a decent motive.
Ultimately your entire motive section could be removed and it would be just as coherent.
I'm aware that at this stage, my theory is based on a series of assumption and still to circumstantial, lacking in hard proof.
But based on Ch 52, Clover seems to have foreknowledge of Yotsuha's time-rewinding powers, and it's only in this loop that they figured out the source is her wristwatch. Seldom does one believe something so supernatural so quickly, unless they've reason to believe it beyond Yotsuha countering them so deftly. Reason like Clover experiencing time travel for themselves.
Same goes for Clover's fast responses when Yotsuha was trying to fix Utako. In particular, according to Yotsuha, Utako also got scammed by Tooya in her previous loop albeit gradually so. This time not only was Tooya found quickly, Utako also managed to be seduced so quickly too... possibly because Clover has knowledge from the previous loop on what pushes her buttons and thus can mess her up quicker.
I admit my motive is also circumstantial, but I had to provide a rationale on how Fuu-chan being Clover could make sense.
Finally using the names as proof is real iffy. I know the Japanese like to use poetic language in their fiction but that's like a serial killer saying he killed people because he's called Steve. Also choosing a nickname based on your real name is terrible opsec.
Me bringing up the names isn't meant to be proof, but Fuu-chan's real name being obscured for so long feels like would carry some significance. "Two" is probably reserved for her for some reason.
"Fuu-chan" doesn't even incorporate opsec, it's just a Yotsuha-given childhood nickname from when they were still in elementary. "Clover" would be the actual opsec.
Although, this is another thing I want to bring up: in their contacts with Yae, Utako and Rikka, the mastermind didn't have to stick with the same Clover icon as their alias, instead of something different each time. Especially with Rikka, the mastermind knows Yotsuha is aware of their presence and still with the hand-delivered letter they insist on the Clover icon instead of using some other alias.
Even at the risk of being caught on,
they insist on the "Clover" alias, why? Definitely feels sentimental rather than logical.