The gist of the spat was both trans rights activists and gender critics were pulling quotes from Pratchett’s work as proof that he understood their side of the argument (ironically the same quotes in some cases) and, as Twitter usually does, the debate got reduced to whether Pratchett would be a huge transphobe or not.
I think it’s clear Pratchett wouldn’t be a huge transphobe, but I don’t think it then follows that he would dismiss all the issues women are raising out of hand as Gaiman did.