Just because some spaces limit speech, doesn't necessarily mean that "every" space limits speech. As you go further down the stack, the fewer limits there are. In the US, in the public commons, there are effectively 0 limits to speech (calls to imminent lawless action are an extremely narrow exception).
The pub vs public park analogy is a good one. A pub is typically allowed to exercise stronger control and moderation over its patrons. The same is untrue for public parks (see: the Westboro Baptist Church). You're correct that HN limits speech, but that's because HN is more analogous to a club/pub; it doesn't purport to be an open platform.
Substack's stance appears to be that they simply follow the law, as they seek not to be a pub, but a public commons by acting as an open platform. And no, investing in certain writers does not automatically turn an entity from a proverbial "public park" to a proverbial "pub".
In my experience as a queer person, lots of vocal pro-trans types take issue with anything and everything.
It's not as though this is an issue of rails, because frankly, in my opinion, that whole activist group has derailed themselves.
I just find it weird personally.