I mean, as an adaption I would like to think Timm would try to stay true to the source material even if it's not like his usual handling of Superman.
I think it'll also depend on who the screenwriter is.
I believe Wonder Woman: Bloodlines was advertised the same way, and that's also an in-continuity movie and seems to be taking cues from Greg Rucka and George Perez's Wonder Woman work.
I could see Brainaic being the main villain like he was for Morrison's first Action arc.
I'm not sure if this is relevant or not but Brainiac was originally going to be one of the holograms Superman fought in that sequence with Wonder Woman in Death before they replaced him with Metallo (I think). So conceptually in the back of their mind they might have envisioned that this Superman had once fought Brainaic.