Yeah I think this is a pretty valid concern. It's similar but more subtle to what explicitly happened at the Economist.
The New York Times would never allow op-eds or culture articles wondering guilelessly whether Jews are actually who they say they are, whether they regret their religion, or indeed if Jewish identity exists at all. They'd never pen multi-page articles tenderly and sympathetically exploring the lives of those opposed to Black people's political and social power. Yet that's totally okay when it comes to trans people.
The Gray Lady's assumptions about the questions that are permissible to ask about trans identity need to shift to match expectations around any other minority identity.