Gender is not a fixed idea.
The principle of gender fluidity underlies everything Sydney discusses about his self perception. It was not necessarily that being a woman felt wrong or out of place, but rather, Sydney discovered that gender felt more like a spectrum, and she felt she would be happier transitioned to a man because that is where she leaned on the spectrum. Therefore, gender would not be a fixed principle for Sydney, because she transitioned out of one gender and into another fluidly without compromising her self.
Working out childhood pains is difficult.
Since there's plenty to talk about, Jonathan and Sydney have a cordial, would-be intimate relationship that grows over the course of a decade. Sydney helps to teach the now grown son why things could not have been the way he wished, and they openly discuss what to do in a confusing, lonely world like this one.
Passion and consequence.
Instead of shrinking back into herself (Sid) and becoming numb or resentful or bitter, Sid detects those emotions and does something about them. When she discovers that it is an option to transition to malehood, she does so. When she finds out that she feels claustrophoic and misused in her relationship, she leaves, regardless of what that might mean for other people. This means that Sydney has had a deeply meaningful experience of life, which she needed, but at what cost?
Jonathan must now wrestle with that strategy in life, knowing what it was like on the other side of Sydney's selfish intentions. This is not to say that Sydney has done something wrong, but rather, Jonathan realizes that the situation is way more complex than he thought, and maybe Sydney did the best thing for herself.
