Sullivan is staking out a position in which he has zero problems with trans people personally, has trans friends who he wants the best for, and because of his personal irl observations of trans acquaintances and friends and his philosophy of live-and-let-live (people know what's best for themselves), he believes that there is an (at least in some instances) essential trans-ness for whom transition is the best possible treatment. I used to have roughly the same position, but I've since moved to the Helen Joyce camp - that trans-ness can't be separated from GI; transition should be allowed as a basic right of personal autonomy and expression (as far as I know she is officially neutral on whether it should ever be funded by the NHS) but as an ideology and identity it is wholly pernicious and invalid, and in her informed (but not professional) opinion transition is never an appropriate medical treatment, even though the underlying dysphoria and distress is real and should be treated as a valid condition. The difference between the two positions really comes down to the question of whether trans-ness can be thought of as a valid identity whose nature sits somewhere between that of homosexuality and psychological pathology (Sullivan) or whether it's invalid. I think Joyce's argument is stronger, but a coherent counter augment can be made, I just find it less logically compelling (though more emotionally compelling).
I agree that Sullivan's command of the issue does not seem to be fully fluent. Perhaps he could be faulted for that. No one can be expected to match Joyce's brilliance - her intelligence and painstaking research are unsurpassed, but it's also no longer necessary to go through primary sources and battle against misinformation (as it stood in the 2010s) to be informed and he was after all at one time the editor-in-chief for a major current affairs magazine; so he's familiar with what's necessary to become fully briefed on a topic.
In any case, Sullivan's position is defensible and it's useful in the debate because it's maximally deferential to trans people and allows him to make a strong argument that trans people are working against their own best interests, as formulated by themselves.
As i mentioned on another thread, Sullivan's main theses is that the authoritarian, censorious nature of the trans debate is the original sin, and to that extent, [LGB]TQI+ activist behavior is an exemplar of the woke left and its threat to democracy, especially since the right is convulsing with it's own authoritarian impulses. Secondly, he makes the veiled threat to trans activists that it will soon be time for gays and lesbians (homosexuals) to demarcate themself from gender ideology and push back against their former allies with new institutions and public condemnation of excesses. Even though many gays and lesbians (i.e. actual homosexuals) feel this way, this is the first time that that threat has been made in the US from a prominent platform, with the NYT as prominent as it gets.