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 scenes like Batgirl hitting on Bruce, which is paying service to the implied relationship 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 DCAU comics, or even Superman: Braniac Attacks as official canon, whereas others don't. That's their opinion, but forcing down your opinion on wants part of the official canon is ridiculous.