"Firstly..."
Where is "secondly" etc?

I am a gay cisgender male who happens to have a trans woman sister in-law and some other trans acquaintances, which has helped motivate to try to get a bit more informed on this than I might have otherwise.

I have personally understood the term "full transition" to approximately refer to a person having taken medical treatment steps to help them appear outwardly typical of their chosen gender, particularly genitalia, otherwise known as gender affirming surgery. But I have never heard anyone claim full transition somehow makes a person biologically indistinguishable from a cisgender person.

But even my understanding has been a bit presumptuous. According to the National Center for Transgender Equality, ...

[What does "gender transition" mean?

Transitioning is the time period during which a person begins to live according to their gender identity, rather than the gender they were thought to be at birth. While not all transgender people transition, a great many do at some point in their lives. Gender transition looks different for every person. Possible steps in a gender transition may or may not include changing your clothing, appearance, name, or the pronoun people use to refer to you (like She, he or they). Some people are able to change their identification documents, like their driver’s license or passport, to reflect their gender. And some people undergo hormone therapy or other medical procedures to change their physical characteristics and make their body better reflect the gender they know themselves to be.

Transitioning can help many transgender people lead healthy, fulfilling lives. No specific set of steps is necessary to “complete” a transition—it’s a matter of what is right for each person. All transgender people are entitled to the same dignity and respect, regardless of which legal or medical steps they have taken.]

You said some contradictions I would ask clarification if you could.

Your statements:
#1. Atheists put reason and facts, over belief and faith. That it is better to live intelligently, then to live in a lie.

#2. Still standing with this, facts and reasons should govern the world, not belief.

#3. Gender dysphoria is a real condition, transitioning helps such people, that is true.

Belief means accept something as true.

On #1 you say reason and facts are put over belief. I can understand reason and facts are important but belief is acceptance of them as true. A person can hold something as true, that is holding a belief, however just because it is believed it is true doesn't make it true. So, when you accept something of reason and facts as true, you then have a belief because you hold them as true.

On #2 it still is about the same as #1 but to point out reasons and facts do govern things of the world but to say it should not be accepted as true sounds contradictory.

On #3 I just point out your belief as you say the statement is true.

You have provided a smorgasbord of ideas. I'll attempt to address them individually,

Point #1: As a common heterosexual male I also fully support "transitioning as a means to help people." If by transitioning you mean any combination or components of drug/surgical/cosmetic/name augmentation etc. to achieve an identity (or perceived identity) that agrees with the sexual identity a person has established for him/her self. I have had two teachers transition from male to female and a student that transitioned from female to male and have no issues referring to and respecting them as their identified gender. I don't understand how supporting this position would in any way be indicative of "bashing someone."

Point #2: "Atheists put reason and facts, over belief and faith" I wish that was the case but not all atheists hold those values. I would also remove "belief" as faith is belief without evidence (redundancy) and atheists, like theists, also believe things.

Point 2.2: "full transition?" Who asserts absolutes? If a woman born with the body of a man and the mind of a woman decides to identify as a woman, fine by me and those I consider worthy of my time. To assert she can not be a woman because she does not have a womb (unless she (and a potential partner) is intent on going through the birthing process) is irreverent. One of my most enjoyable encounters I remember like it was last night was a decades ago meeting after class and going on a long evening dusk into the darkness of night walk by the river with a lovely (her mind was sharp and kind) transitioning woman. If she was not leaving the state the next day I would have perused a lasting relationship.

Point 3: To reiterate, from my perspective, "full body transformation" (including x y chromosome?) is not necessary to establish an identity relevant to the gender one's identity.

This talk may be worth your time.

Thanks for sharing.

I have never heard anyone suggest that a full, biological transition was possible. In fact, I've heard many, (mostly transphobes,) insist that full biological transition is NOT possible (true) and that therefore transitions should not be recognized at all (not true, in my opinion.)

Personally, I don't see a problem with recognizing the transition socially, and ignoring the biological stuff in social contexts.

"There has been a notion that men can biologically transition fully to a women and that women can biologically, fully, transition to men."

I have not been aware of any such notion, and do not know anyone who believes in such. But, I am not all that tuned into issues of gender, so perhaps have missed something.

What I do understand, is that gender is poorly defined and is far more complicated than X and Y chromosomes.

Having a womb or testicles is not the defining characteristic of being a woman or a man. People can lose those parts of their body due to disease or other factors and some people aren't born with a full set of functioning sex organs. My own mother no longer has a uterus so I suppose for you she is no longer a woman.

Also, on a genetic level, you are not 100% a man or 100% a woman. Technically, you're about 97% of one gender and about 3% of the other.

I'm not transgendered and have no intention of becoming such so I'm quite sure a trans person could explain this much better than I ever could. But, from my understanding, being transgendered isn't about becoming 100% biologically a different gender. It's about living ones life as they choose, both mentally and physically as best they can. Why would I oppose that just because I'm an atheist?

Fully becoming a man or woman differs from having been born so. You're splitting hairs for no purpose.

There seems to be some confusion on my part. Thanks for further explaining. My 16 y.o. son helped me understand some of this also.

OTOH....I don't really have an opinion or valid argument to make either way. Still learning, I guess