The Atlantic piece by Helen Lewis that you criticised does explain the silencing of gender critical women:
"As [JK Rowling] wrote last year, she has grown accustomed to “threats of violence, to be told I was literally killing trans people with my hate, to be called cunt and bitch and, of course, for my books to be burned.” The former Scottish Labour leader Johann Lamont told me that, in her assessment, many of the angriest voices against gender-critical feminists like Rowling were male allies of transgender people, rather than transgender people themselves. “I see young women silenced … I see young men emboldened and empowered,” she said."
"Cherry and McAlpine, the two most outspoken and high-profile internal party critics, have been ruthlessly marginalized by the SNP hierarchy: Cherry was sacked from the party’s senior team at Westminster, while McAlpine lost her place at the top of a candidate list after an SNP committee ruled that it should go to someone who identified as disabled."
And she criticises policy-making that goes along blindly with TRA's demands:
"What is driving the SNP’s behavior? In the case of equality legislation, many of its activists believe that gender self-identification is the great civil-rights struggle of our time. Another explanation is that the party’s hegemony is so assured that its leaders live in a hall of mirrors, with NGOs and lobbyists reflecting their own opinions back at them. Big charities rely on the Scottish government for the bulk of their income, encouraging them not to rock the boat. It was considered radical when McAlpine invited grassroots feminist groups and gender-critical academics to give evidence about recording sex data in the census—instead of relying solely on charities such as Engender, which receives £275,000 of its yearly £355,000 income from the government. She had broken the hall of mirrors."
The article is not perfect but Helen Lewis was speaking up on this when nobody else was, and getting abuse for it.