Mystery of the Batman came out in the middle of Justice League, when the DCAU was running strong. Alan Burnett and Michael Reaves both stated in a featurette that they tried their upmost to fit it into canon, that's why they included pointless scenes like Barbara hitting on Bruce, which is paying service to the relationship that was implied in Batman Beyond.
Batman and Harley Quinn is meant to be a weird, off kilter standalone film that pays homage and has easter eggs for old school B:TAS fans.
https://youtu.be/2QpTNl2wkaU?t=158
Could the film be canon? Sure, but it's up to personal interpretation. Some people consider the cutscenes from The Adventures of Batman & Robin video game as a "lost" episode from TAS, or even consider Superman: Braniac Attacks as official canon, whereas others don't. That's their opinion, but forcing down your opinion on whats part of the official canon is ridiculous. As Tupka said, we can't just pick and choose.