It is probably the best Guardian article I've seen for a while.
I think Clara Barker is beginning to try to understand, which is a start, but there's an argument that Barker is using which I see all the time, and which needs questioning:
“It is held against me that ‘you were raised with male privilege’, but actually I was beaten up all the time for being effeminate,’” says Clara Barker, a trans scientist at the University of Oxford, who also leads voluntary work with LGBT young people. “Because I was trans I was severely depressed, I was bullied in my workplace, so it’s like, ‘What privilege is that?’”
Just because you had a shitty time as a boy and a man, and experienced homophobia, that doesn't mean all your male privilege is negated. You still have male privilege, just as, say, while people who were born into poor families still have white privilege, however shitty a time they had growing up. Being disprivileged on one axis doesn't magically remove your privilege on another.