100% this. Timm has had a couple instances where he was more solid with whether its canon or not. "it was just an excuse to kind of go back to the BTAS world" or "I personally kind of think of it as a continuation of Batman: The Animated Series, and the DC Animated Universe", but people keep pointing to the ones where he was a bit more iffy about it. Even then, he adds the caveat that he's "not actually in control of what’s in continuity and what isn’t" basically implying that's up to corporate to decide.Personally I think Bruce Timm is either overthinking things or underthinking things. But his unsureness has to do with the fact that there have been several DCAU projects that he had nothing to do with that are considered DCAU canon. But the reason they are considered canon is because the producers of those projects did everything in their power to make them fit. If the same is true for Batman and Harley Quinn (and it doesn't actually contradict much if anything from the canon) than that's good enough. It's not simply that DC holds actual power over which canon is official. But the official stuff is by creators who went out of their way to make it fit.
WB billed the movie as "Bruce Timm returns to his Batman: The Animated Series roots." DC has the film as a Batman: the Animated Series movie on their website, and on the back of the trade collection of the movies tie-in comics theres a blurb that says "Head back to the universe of Batman: The Animated Series in Batman and Harley Quinn". So it seems very clear where WB/DC stands on its canonicity.