The custody trial did not litigate the fact of whether or not he abused Dylan. It simply wasn't the issue before the court. And since that was the case it made the custody issue a lot easier.

In short, Allen was already in therapy for acting inappropriately towards Dylan.

This is not actually the case (This is because you need find the actual testimony that occurred to get the full flavor of this case.) This therapist was a psychologist who specialized in children and her primary patient was Satchel (now Ronan) Farrow, but she was familiar with family dynamic

The psychologist, Dr. Susan Coates, also testified that while she considered Mr. Allen's relationship with his own adopted daughter, Dylan Farrow, to be "inappropriately intense," the therapist never observed him acting in a sexual way toward her. And she reported that an evaluation of Dylan conducted in 1990 found the girl easily "would be taken over by fantasy" when asked to describe something as simple as an apple tree.

The testimony of Dr. Coates -- who regularly treated the couple's biological son, Satchel, from 1990 to 1992, and often conversed or met with both parents -- appeared to provide an alternative explanation for Mr. Allen's behavior toward Dylan other than the one advanced by Ms. Farrow. The actress's accusation that Mr. Allen had molested Dylan at her country house last Aug. 4 is a central issue in the custody trial in State Supreme Court in Manhattan.

Here's the full quote of what she said.

Coates will testify, “I did not see it as sexual, but I saw it as inappropriately intense because it excluded everybody else, and it placed a demand on a child for a kind of acknowledgment that I felt should not be placed on a child.”

https://www.thenation.com/article/woody-and-mia-modern-family-timeline/ This link is a very good timeline of the facts in this case.

The therapist who was apparently more on Allen's side ............. Obviously she'd be motivated not to see that, given who he was and that at that time there weren't accusations of actual abuse against him.

There's no basis to say this therapist was on Allen's side as opposed to be on the side of the truth. She knew Dylan quite well and had examined her previously. What would she not be on Dylan's side?

The Farrow side basically dismissed any professional testimony that was against their case as biased towards Woody Allen. They never did explain why the doctors would not be biased towards the child in a case of actual abuse or biased towards the truth. They only became biased after they gave their opinion. Dr Coates was first doctor called Mia Farrow called about this accusation.

I have no idea how you could speak to the doctor's motivations, let alone her obvious motivations. There's no reason to expect her to be biased. And you are wrong, as to when she made these comments. This was testimony under oath at the custody trial. This was months of after the original accusation of abuse that Dr. Coates was the first medical professional to hear about.

There is still to this day, only a single accusation. And none of the doctors or psychologists involved in this accusation would say that any abuse occurred which is why both NY and CT concluded no abuse occurred.