This might be a long shot, but the Ben Affleck Batman has a lot of similarities to the Tim Burton/Joel Schumacher Batman Universe!
WARNING: Spoilers ahead for 'Batman V Superman: Dawn Of Justice.'
1. They're Both Murderous Lunatics!
In Batman (1989), Batman just kills everyone with no regrets. If you want to get nuts, he'll get nuts!
Also, Affleck's Batman kills mostly everyone. He even uses guns not once but twice! Excluding the dream sequence! Now, I know what you're thinking: The Joker died! How can there be a Joker in Suicide Squad if he died?
2. There Are Two Jokers!
After Batman brutally murders the Jack Nicholson Joker, a new Joker pops up years later to continue his legacy. That would explain those self-referencing tattoos. He drops himself in the chemicals that gave the first Joker his white skin and such, then gets the tattoos because he loves everything his predecessor stood for. Also...
"Maybe it's just Gotham City and me. We just have a bad history with freaks dressed like clowns." - Bruce Wayne
He clearly states FREAKS. Plural. FREAKS dressed like CLOWNS! Plural again. He was talking about the two Jokers. He couldn't have been talking about Superman because Gotham didn't have a bad experience with Superman.
3. The Timelines Line Up!
At the start of Batman (1989) people thought of Batman as a myth to scare off criminals. So that means he was just starting out, because a lot of people had yet to see him. Now, in Bvs:DoJ everyone knows he is real. Also, Batman is older than the Batman in Batman (1989). You must be thinking that if the suit and equipment look different they can't be the same!
4. The Suit Changes In Those Same Films!
In the Batman Universe the suit and equipment constantly differ, going from pretty slick to holy nipple grease, Batman! The Affleck suit must have been the latest version.
5. Batman Didn't Know About The 'JLA' Members Until 'BvS:DoJ'!
In the Burton/Schumacher Bativerse there was no mention of the other heroes. Affleck's Batman just found out about them in his movie. There was a mention of Superman in Batman & Robin, but that could have been happening slightly before Man Of Steel.
Because Superman was doing stuff before he was wearing the costume!
He was traveling the world and there is no chance he wasn't noticed. It was said that everyone in his town new about him when he was a child. Also, Batman & Robin was probably close to Man Of Steel because Dick Grayson was Nightwing already so he could have been training another Robin in secret for the new Joker to kill! Because a single film can't cover everything, maybe the Jared Leto Joker was milling around already.
6. Harley Matches The Timeline!
With the Jack Nicholson Joker, Harley didn't come out. So maybe she didn't fall in love or even know the first Joker. So she met the Jared Leto Joker and fell in love with him instead. So she could be a kind of a recent threat.