If anything, the roles should've been reversed: have the Suicide Squad game be in an alternate universe so Batman can still appear as he should (they ARE Batman villains, after all and the '89 Batman logo never appeared in the Arkham games,
just sayin') without wrecking the Arkham continuity and, and I shouldn't even have to point this out, but Gotham Knights should've been the game to pick up where Arkham Knight left off, not the other way around. You have the Bat Family taking up Bruce's reigns after he "died", which the AK post-credits scene seems to have confirmed he faked all along (the bat-silhouetted figure had to have been Batman taking out the goons, or it just as easily could've been Red Hood, in which case, it still sets it up perfectly), so it makes perfect sense for Bruce to hire them in the shadows to combat the uprising crime following his "death" while he distances himself from his now tarnished image and life as Batman similar to The Dark Knight Returns' ending.
In fact, it doesn't even have to be one or the other. They could've had them both be set in the Arkhamverse, but made the Suicide Squad game a side story much like the Miles Morales Spider-Man game. It still would've meant no Batman, but Harley could gloss over and address his "death" with the rest of the gang, even casually bring up the superhero team he was apparently apart of as a hook. I believe the goons even referenced Superman and/or Metropolis at one point in Arkham Knight, so it's not like they don't have anything to build off of for an Arkham Knight continuation even if said honor should've belonged to Gotham Knights.
Hell, correct me if I'm wrong, but I'm pretty sure they even used the same news clip of the reporter lady reporting his "death" at the end of Arkham Knight in the Gotham Knights trailer, so this will just make it extra confusing for players who are obviously expecting a continuation of the Arkham Knight story. Sure, he's "dead" alright, but his "death" in Arkham Knight technically never happened in this game's timeline like casuals would reasonably expect. Good luck explaining that one to fans who don't read the gaming news sites.