Before I begin, let me state that I am no expert here. But your post caused me to reflect and research a bit and what I learned made me realize certain things that you may wish to also consider.
First, you may wish to consider whether a living relative who is not your ancestor wishes to be included in WikiTree. That should always be a person's choice.
Second, even with profiles of non-member living individuals remaining private, the information now exists on a server which, like any, is not an impenetrable fortress. Website hacks happen every day. I would advise keeping the information that you store on WikiTree to that for which there would be zero potential repercussions if it were to be released publicly.
Third, for many transgender individuals they consider their status as a transgender person to be private. Even governments have recognized this legally for those working in an official capacity:
It cannot be stressed enough that everyone has the right to privacy. A person’s transgender status should always be treated with the same high level of confidentiality as any other sensitive personal information.
Some people may be happy to have certain people know they are transgender, but not for some others to know. Therefore, even if they appear open about their transgender status, always leave it up to the trans person to decide who they wish to tell. Revealing someone is transgender (‘outing’ them) not only violates their right to privacy, it also places them at risk of discrimination and harassment. It can sometimes even place them at risk of physical or sexual assault.
The Gender Recognition Act 2004 defines any information relating to a transsexual person’s gender recognition application as ‘protected information’. It is a criminal offence for anyone acquiring this protected information in an ‘official capacity’ to disclose it to a third party without the transsexual person’s consent. There are a few exceptions, for example if the information is required by the third party for the prevention or investigation of a crime or if the information is needed by medical professionals at a time when the trans person is too ill to be able to provide consent.
While that may not apply to us in any legal sense, I believe that such may apply in an ethical or moral sense.
There is a strong privacy consideration not only because such changes are deeply personal, but also because there have been many instances of people being subject to violence after having their transgender status revealed publicly by others. The Human Rights Campaign has documented several transgender persons whose status may have been a factor leading to their violent deaths. In other cases there is a strong connection between public, non-voluntary outing, and the suicides of transgender persons.
While WikiTree's culture is largely one of tolerance (and we can be thankful that intolerance and hate have been exhibited by members only on the rare occasions), one cannot know the private thoughts and intentions of those who have access to private data on WikiTree. So no matter what, even if the profiles are private, there are some people on WikiTree who have access to that private data and you cannot know for certain what they may do with it. The few whom I know, I trust reasonably well, but with such private, personal data, it may still not be appropriate to entrust them with it.
Fourth, as per WikiTree's current policy, "A person can only have one gender on WikiTree. Therefore, if a person's gender changed during their lifetime, a choice will need to be made." By creating a profile for such a person, while living, you may be taking that choice away from them.
So for all of the reasons above, I were I in your shoes, I would have a chat with each of them in person and ask if they are comfortable about being included, and if so, how they will be represented. If they are not comfortable, then simply don't add them. It really should be their choice.