He was a Keaton Batman, sure. '89 and Returns happened to him, but in a totally different world.
That's what he was explaining to the Barrys, and why he compared it to spaghetti. Barry's time travel caused timelines to intermix. Michael Keaton's Batman is not supposed to inhabit a world that eventually became just like the Snyderverse. General Zod was not supposed to arrive and destroy everything. What we're seeing in this movie is a new universe... and the Batman who shows up at the end is proof that the timeline is still jumbled up, now it's just jumbled up in a way that wasn't a total disaster.