For years in this series, it is said that "Bruce Wayne" is the mask for Batman. "Bruce" is the mask he wears in the light to hide his true personality and beliefs. Now, consider the title of the movie, "Mask of the Phantasm" isn't just trying to be scary about the titular character. It refers equally to like Batman using "Bruce", the mask of the Phantasm is "Andrea Beaumont." Like Batman, Phantasm uses the appearance of a socialite person to move by people who have not earned her vengeance.
Why is Andrea able to so conveniently arrive to save Batman from the police pursuit? Because she was already there, fighting him as the Phantasm just minutes before.
Similarly, why do we see the Phantasm first in the opening action scene, then get a scene soon after of Andrea actually arriving in Gotham? From a meta sense, it's to stop us from considering her a suspect, but in the reality of the film? Simple: she was covering her tracks. She was talking to Arthur on the phone at the time, ensuring he could provide an alibi that she wasn't 'in town' when the Phantasm first struck, but how do we know that for sure? We have no idea where she was flying from, it could have been from the next city over. This way if anyone accuses her of being the Phantasm, her doting wannabe-boyfriend Arthur can leap to her defence. No wonder she kept buttering him up throughout the film, he was her bulletproof alibi.
Why do Batman and the Phantasm not fight each other directly, even before we know who the Phantasm is? Because as revealed with Kyodai Ken in the series, fighting styles are as unique as fingerprints, and the two have fought (sparred, really) in their civilian identities before - in an extended battle, Batman would have realized who the Phantasm really was!
That and Bruce would've overpowered her fairly quickly. She's capable, but her successes relied on misdirection: tricking Chuckie Sol into driving of a ledge, tricking Buzz Bronski into falling into an open grave then dropping a statue on him. note We only see the statue dropping, and the spot it was one is obscured by trees and shadows - she used leverage, not just raw strength. She tried to kill Sal Valestra outright, and his smoking habit had long devastated his body. That said, she might've been able to kill Joker in a straight fight, given that he ran from both her and Batman when showed they could beat him.
In the series episode "Paging The Crime Doctor", Batman and Alfred find the titular doctor's med school photo album. Said album shows he was a classmate of Leslie Tompkins and Thomas Wayne, which recognizes was 40 years ago. Said album was dated 1908. If the movie takes place after the series, this puts the present day segments in 1949, meaning Bruce first donned the cowl in 1939, probably the exact same date he first appeared in the comics.
The song "I Never Even Told You" by Tia Carrere doesn't make sense in terms of Bruce and Andrea's relationship. After all, the entire film was about how they loved each other and told each other so. So, who is the song about? And then it hits you: it's about Bruce and his parents. It was a sudden, brutal murder. The way they were killed never gave Bruce a chance to tell them he loved them or even goodbye. Bruce's parents never got to say goodbye or tell him they loved him. Their deaths hang over the entire film, too—Bruce is looking for love and acceptance, because he never got closure with his parents. It's the entire reason he's Batman. He was willing to toss away being Batman because of love. All of which is denied him in the film, all stemming from not having that closure.
