Well, to be honest, I'm not sure that makes a difference.
And that's mainly because from the perspective of someone who is transphobic, there is no such thing as a true transgender person. There are only "mentally ill people" who have been "brainwashed into thinking they are the opposite gender" or "perverts" and "sexual deviants" whose entire goal in life is apparently to "coerce people into sleeping with them" or otherwise "force 'normal' people to indulge their 'disgusting' sexual fantasies".
In other words, as far as a transphobic person- or even an everyday person who could care less and is generally ignorant about transgender people is concerned- any character who goes out of their way to crossdress and impersonate another identity can come across coded as "transgender". All the more so if they fall into transphobic stereotypes they may have distantly come across.
A part of me wants to say that so long as the creator's intent isn't bad, they shouldn't be held responsible for how people interpret their work. I certainly hold no real animosity towards the creator of something like Box Trolls. They probably fell into this controversy entirely by accident. I like to believe in creative freedom in general.
On the other hand, there are many popular misconceptions about transgender people, and very few actual transgender people to go around. Most people will never meet a transgender person irl who can debunk all the bizarre ideas floating around out there simply by existing around them. This means transgender people regularly end up in situations that range from uncomfortable to discriminatory to downright dangerous. So it's very hard to discount even well-intentioned mistakes as no big deal when media portrayals may be the only exposure to transgender people that most people will ever get.
Of course there's also something to be said here for me not giving people enough credit. I would like to think most people can tell the difference between a transgender person and a "villainous crossdresser" in a children's movie. It's just that my everyday experiences tell me that's not necessarily the case 