Anon, I agree with everything else you said. I've beaten the drum for Flashpoint loudly and proudly, but not without context. The only reason I mention it is because WB announced it as what they were planning this past season. Without that I wouldn't even consider it for a third Flash movie.
Personally, I've insisted WB take the clean slate the end of JL feels like and give everything but Wonder Woman that preceded it the coldest shoulder, and do everything to ignore them and their content not related to source material as thoroughly as possible. Don't do origin stories for the League, and jusr drop all of them into their established careers as superheroes. Rename the MoS franchise as Superman, and identify the sequels to it and Justice League with subtitles instead of numbers. Produce all but Batman and Aquaman to a lesser degree with different tone, aesthetic, and cinematography than what we've been given. I think doing this accomplishes 95% of the work of spiritually retconning MoS, BvS, and SS.
If done effectively, nothing would need to be said or done publicly to make the message clear to the public.
What would be left is the deaging and recasting of Batman, which Flashpoint would facilitate better than anything short or canon usage of a Lazarus pit. I'd also personally like Superman's background to be tweaked a bit, but that could be referenced in the next Superman solo movie, ideally not via flashback.
If origins are going to ignored overall, then just drop Flash into a movie with the Rogues, and allow the background and code of the Rogues to be established via discussion among the police, and within the Rogues after Heatwave going to far. I don't think the concept of a pack of thieves that uses meta-like tech in a world where metas appear in public without fear, is a hard sell. Combine that with Barry still being green out of JL, and make the movie about his starting to master and get better with his use of the Speed Force.