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I'm modifying a genealogy (updating an old, written one, that is) which includes a trans man. We will have him listed as male (of course), and will not be recording the (apparent) change in gender (from female).

I'm unsure of how or if to note his name change from a very female-sounding name to a very male-sounding name. This also includes a change of last name.

I'm thinking of doing this in the same way we do other name changes:

"John Smith (nee Ellen Brown)" or something along those lines. This would also not record the year in which the name was changed, which is fine by me. My concern is that this is "dead-naming" him, which is generally looked down upon. The alternative is to not note any change, but I'm afraid that could be confusing to people who don't yet know of the change.

Any ideas on how to proceed?

I have a similar circumstance in my family tree. It may be relevant that this was in England and Wales (where I believe that, if somebody applies to be recognised officially as another gender, previous records are unavailable. So, except for the fact that I sought his records in a very narrow time window, the records would not match what I know.

I recorded him as male (Obviously). I asked for permission (and received it) to identify him as the child of his birth parents, with a note about his name change

To the degree that he consented (or didn't consent) I would keep the details (name change, birth name, current name, birth details) confidential. If he didn't consent at all I wouldn't have recorded them.

Likewise, I would not record his birth name and current name without his agreement (to avoid deadnaming him ).

In summary: ASK HIM.

The ethical way to proceed is to ask living persons their consent before adding them to a work of genealogy. Just as you wouldn't use a living person's DNA sample without explaining the purpose for which it would be used, and securing their informed consent, you should talk about these issues with the living person whose information you want to include.

Names:

You say:

The alternative [to dead-naming him] is to not note any [name] change, but I'm afraid that could be confusing to people who don't yet know of the change.

If you are considering 'outing' someone, then you most certainly need to stop and think about what you are doing, and talk about the issues with the living person. The PFLAG National Glossary of Terms says in their entry Coming Out:

Not everyone is in the same place when it comes to being out, and it is critical to respect where each person is in that process of self-identification. It is up to each person, individually, to decide if and when to come out or disclose.

In the section Disclosing Birth Names, the GLAAD Media Reference Guide - In Focus: Covering the Transgender Community says:

Do not reveal a transgender person's birth name without explicit permission from them.

Gender:

You talk about not including a "change in gender (from female)". This language usage describes the point of view that someone might take if they were only looking at the historical record, not considering the life of the actual person. Most people wouldn't speak of a "gender change" if an infant was mistakenly marked as a 1-month old female in a census record but was marked as male in all their other census records -- it is conflicting evidence that needs to be taken into account as part of the Genealogical Proof Standard, but most hobbyist genealogists would say that the gender assigned to that member of the household in that first early census must have been a mistake.

Record creators in the past may have assumed a gender or assigned a gender that does not reflect the lived experience of that person. Strive for precision and clarity. Avoid usages such as "on the census [a person] said". We rarely know who gave the information that appears on a census record.

See the entries in PFLAG's glossary Assigned Gender and Assumed Gender. Consult the living individual about whether or not to include information about the gender assigned at birth, and the language that you could use to describe that information.

Ethics:

We don't have to be professional genealogists to benefit from the standards and ethical guidelines used by the pros. The Association of Professional Genealogists Code of Ethics and Professional Practices says, under point 9:

[I agree to] [t]reat information concerning living people with appropriate discretion

The BCG's Genealogists' Code of Ethics says:

I will keep confidential any personal or genealogical information disclosed to me, except to the extent I receive consent to share.

The National Genealogical Society's Guidelines for Sharing information with Others recommends that family historians and genealogists consistently:

• inform people who provide information about their families how it
may be used, observing any conditions they impose and respecting any
reservations they may express regarding the use of particular items;

• require evidence of consent before assuming that living people are
agreeable to further sharing or publication of information about
themselves;

• convey personal identifying information about living people—such as
age, home address, genetic information, occupation, or activities—only
in ways that those concerned have expressly agreed to;

• are sensitive to the hurt that information discovered or conclusions
reached in the course of genealogical research may bring to other
persons and consider that in deciding whether to share or publish such
information and conclusions.

The Code of Conduct/Ethics of the International Association of Jewish Genealogical Societies says:

Generally, requests made to genealogical researchers should be respected when individuals ask that certain information about
themselves or family members be kept private.

In short, the ethical standards of the day all recommend the same advice that was already stated in the previous answer. Ask living people what information is appropriate for you to include, and ask what language usage is acceptable to them. If your trans interviewee asks you to use the term "gender assigned at birth" rather than talking about a "gender change" then use the requested language.

Further reading:

• 
  Ethical guidance by by Judy G. Russell, posted Aug 24, 2017 on her blog The Legal Genealogist
  


• 
  Genealogy 101: Ethics for the Genealogist by Gena Philibert-Ortega, posted June 7, 2019 on the Genealogy Bank blog


• Cyndi's List: Etiquette & Ethics » General Resources
  


• FamilySearch Wiki article, excerpted from course material by NIGS: Genealogical Ethics
  


• Genetic Genealogy Standards