Them going with Flashpoint doesn't necessarily say "we're retconning", but it says "we're going with the biggest Flash story we got straight from the gate"; I've mentioned before why Flashpoint makes sense from a story/character point of view (irresponsibly changing reality because of going back in time for personal reasons sounds more like a rookie mistake than one an experienced Speedster would make), and also it offers something new to the audience instead of yet another "origin" movie.
I know a lot of people wanted a more "low-key", Flash vs the Rogues type of movie (and I thought I wanted that too), but I think if they did that, I'd feel about pretty much the same way I feel about Spiderman: Homecoming; sure, I'm sure it well made and all, but there's nothing about it that I feel is new and exciting enough that I MUST watch it now, ya know?
Just my take.
I agree with you that it works well as an origin story generally speaking.
If it sticks to Barry's point of view and doesn't delve too deeply into the negative consequences to other characters, then it could be a clever way to tell Barry's origin story, his life story really, while still setting it post-JL. Meaning, Flashpoint is essentially a more enhanced version of the email device from
Wonder Woman.
I will say, though, that I have zero desire to ever see anything from the Knightmare world and would prefer any Flashpoint movie to be as Flash focused as possible. To me, Barry's warning and Bruce's nightmare were separate things, and only Barry's warning came from the future. Moreover, with a victory in
Justice League, whatever bad things had happened in that Barry's world should be a closed time loop that created a better alternate timeline for our characters. If the BvS incident has to be addressed, let it be something Bruce informs Barry of in JL. That way, it will make sense why Barry, in his own later movie, starts to be tempted to travel through time when maybe he hadn't known it was something he could do until Bruce told him a version of him did.
Obviously part of Flashpoint requires Barry to change things only to realize his error and change it back. To recognize it as an error, what he creates has to be so terrible and so wrong that it requires fixing. In
Back to the Future 2, Marty doesn't spend a whole lot of time in the darker 1985 timeline. So, my choice would be to have Barry only briefly encounter scenes reminiscent of the dark timeline in the comic. I'd also prefer if the film version tried its best to incorporate Kiersey Clemons' Iris West, and not have Barry simply be a lone time traveler fueled by grief and regret.
As for retcon speculation, I'm not sure how Flashpoint could really accomplish much. For example, if people's criticisms of Snyder's Superman and Batman is that they responded a certain way to certain stimuli, changing the stimuli to produce different results won't change the fact that we know they have the potential to do those things given certain variables are in place. Other changes wouldn't be minor, and as a result, would undermine the logic of the narrative. If, for example, Zod isn't killed. Doomsday never happens, and so on. Changes, then, if any, would have to be minor. Clark Kent can exist again perhaps.