Dr Ruth McNair is a member of the Victorian Government's LGBTI taskforce and is one of few experts working in the transgender space in Australia.
She, like others, was not consulted by the AFL before it made its decision to exclude Mouncey from this year's draft.
When women transition they take female hormones as well as testosterone blockers.
"Many trans women affirm their gender by using female hormones … so in trans women the testosterone level is usually suppressed well into the female range," Dr McNair says.
"Most transgender women get into that female testosterone range within the first couple of months of using estrogen … it stays in that range for as long as they continue their hormone treatment."
The big question is whether there is some overlapping benefit of having had the advantage of male levels of testosterone in the years leading up to a person's transition.
"The only benefit is the body shape that developed due to testosterone during adolescence," Dr McNair says.
"So trans women have developed their bodies in a masculine frame so they might have a larger bone mass and be taller, but in general that's the only ongoing effect … [due to treatment] their muscle mass and strength is reduced."
The AFL, in this week's decision, cited concerns of stamina, strength and physique.
Dr McNair believes the medical evidence does not support that view.
"No, I don't. Obviously with physique, Hannah can't change that, but the strength and stamina will have altered due to her hormonal treatments," she says.
It's a difference Bagger can attest to as she embarked on her professional golf career.
"I did notice [after transition] there was a significant difference," she says.
"I'd go and play the same golf course — and even playing from the same tees — I noticed I had to use a completely different club, so the change is very real and very significant.
"It does take a period of time, I'm not sure of the quantifiable length of time, obviously two years is one that's used a lot at the moment in most policies, but it is a gradual and very real effect on the body."
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US-based medical physicist Joanna Harper, a trans woman and competitive runner, has written an academic paper on transitioning and the impact on sports performance.
"When I started to transition in 2004 … within nine months I had started running 12 per cent slower than I had been before and men run 10-12 per cent faster than women — and so in nine months, I had lost all of my male advantage," she says.
"I have spoken with Hannah off and on for over a year now and Hannah is absolutely a large, strong woman and transgender women are on average bigger and stronger, so of course transgender women have athletic advantages, but they also have disadvantages too.
"So the question is, can transgender women and cisgender women [those who identify as their sex assigned at birth' compete against each other in an equitable and meaningful competition?
"The science says 'yes'.
"Specifically with regard to Hannah, she's big … but one of the things is that she has a large skeletal system which hasn't reduced in size, but her muscles have substantially reduced in size and strength.
"So she now has a female-size engine trying to move this big skeletal frame around and that is going to cause her some substantial disadvantages."
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Sports lawyer and gender equity and diversity specialist Catherine Ordway believes the AFL may be concerned about the legal repercussions of allowing trans women to play in the AFLW.
"That is the only argument I can imagine the AFL is running through to come up with this decision," she says.
"That they're concerned on the behalf of the other players, that they may be at higher risk of physical injury on the field.
"However, the fact is, Hannah has been playing in the local league in Canberra for the last season and her coach has publicly said that there hasn't been any issues, and from what he's observed there's no reason to think that there would be and the risk would be extremely low, if at all.
"In this particular case I can't understand why the argument would be that the AFL women are not strong enough to cope with playing with or against Hannah and yet it's OK for what is presumably a weaker competition in the local league for Hannah to continue to play.
"That seems to me to be a contradiction that they can't support."