Hey, enby here. While I definitely benefit from they being a default I have enough binary trans friends who have this experience. What the person you are replying to is giving you is something referred to as nuance. A solve put forward by a well meaning cis person doesn't automatically work just because it seems like it should to you. Sometimes it causes new problems and when someone tells you about them it's a good idea to not assume it's them trying to be a dick or difficult about something but actually explaining why that solve isn't always a good thing.
If your intention is to make a trans person actually comfortable instead of getting defensive then listening when these things come up instead of telling them they are trying to be trouble on purpose is the play.
Not everything works for every trans person and inside the trans community there is something sometimes referred to as "the coward's they". It's a well known phenomenon where a physical transition gets to a certain point the brain stops easily registering and sorting someone as being their birth sex because they seemlessly look and act as their gender so the automatic neurological system of assigning them a sex value flips fully to the new and desired setting. You see it on conservative media sometimes where they slip up and use the actual correct pronouns and have to correct themselves back over to using the wrong pronouns... Problem being is it causes the same mental redirect issues for a Conservative actively dodging the automatic reaction as learning to use Non-binary pronouns so as a compromise these people use "they" instead because it is easier to trick the sorter and strand themselves in the safe neutral ground where they can identify a person as "not actually a woman/man" without triggering their audience by using correct pronouns for a trans person.
When you use they/them pronouns for a binary trans person it's interpreted by the brain of the trans person as you seeing and reacting to all the aspects of their body that makes them visibly trans and your brain's automatic sex recognition system sorting them into this "not enough" category. It's effectively less hurtful than full misgendering... But it still pings the bit of the brain that is seeing their own body through your perception via your words. It causes they same dysphoric reaction where their mind picks over all the parts of their body that would cause you to react by misgendering or degendering them. The whole point of preferred pronouns is to help us stop that mental reaction from happening as much.
It is perfectly safe to use they/them pronouns for cis people who do not have dysphoric reactions at all and for non-binary people who actively use those pronouns but if someone rocks up looking like they are trying to project a full binary situation it's worth going for the full binary pronoun option because they are specifically putting in the work to be as obvious as possible so that people know that's what they want.
Hey, Non-binary trans masc person in trades here.
I can tell you how I perceive different types of co-worker if it helps you want to dial in what it's like on the other side of the experience. There's layers to the whole situation and as non-binary folks we understand what we are asking for isn't automatically going to click and requires people to figure us out.
First up : Most of us end of day aren't going to rock the boat for anything less than fully agregious behaviour so calls to report other people for being mildly offensive are probably not actually going to go anywhere. Most of us are scared of being labelled "a problem" so we just take the hits when they come. If you are a boss and notice a non-binary person sticking closer to specific people and avoiding others there's a good chance that they've found the people who are safe and avoiding ones who aren't. A great accommodation that can invisibly help is just to recognize this strata and if a task nessesitates putting people together try and pair along these lines. A lot of co-workers wait until other people aren't around to let their nastier behaviour shine.
Now to co-worker types. Aside from the full on transphobe or problem persons there's a range of different stages of cool people.
The "I don't really get it" Co-worker pays lip service to the polite aspects of using pronouns. They are the type to introduce you to others by misgendering you and then flap their hands and go "Oh no sorry 'they'". We know they don't get it or don't really care. The misgendering still hurts but they are fairly benign. They make these accidents non maliciously and are afforded grace. If they step in it we basically disregard because they aren't really worth the effort of getting too comfortable around. We make these accommodations for strangers daily. Annoying but nessisary.
The "in training" co-worker is one whom is encountering their very first trans person. They want you to be their Obi wan and their enthusiasm is a bit of a double edged sword at times. It's tiring to teach people to dance when they keep stepping on your feet but the job needs doing. Some of us veiw this as our own brand of service to the cause of normalizing ourselves more widely. Some of us just don't want to be bothered. Either way, just wanting to learn is heaps better than ambivalence. If you fuck up something, don't make a big deal about it. It's not that you're a terrible person and should have known better. Our stuff takes practice and we know it's not intuitive.
The "A little too up in our shit" co-worker is excited to know the real you but looks at you as a beautiful creature in need of preservation. They might seek to advocate on your behalf or behind your back but the attempt is clumsy and often at odds with a non-binary person's desire to just get through the workday as a regular human and not make waves. Good enthusiasm sure, we're probably friends but for the love of God we're adults and we can sort out our own shit if need be.
The "Understands the Assignment" co-worker is just comfortable to be around. They don't have to be the most tuned in to all the nuance about our specific needs in ways we require more out of partners, family and friends but they treat our basic requirements as no big deal, maybe they occasionally ask questions to check in if they catch us struggling or reacting but aren't going to narc to the boss on our behalf. They either avoid all stereotypes associated with sex or in the case of trans mascs/trans femmes they treat us like one of the boys/girls. Gold standard.