Shadowstalker16: Lets recap. Gender is another term for sexual orientation. Sex is the physical characteristics(of the genitals) of a person's body.
Gender dysphoria or transgenderism / transsexualism comes about when a baby in the womb receives unbalanced level of sex hormones to his / her brain and body. So the brain may receive testosterone and the body, estrogen. This will lead to a feeling of a person being trapped in the wrong body, a la gender dysphoria. Basis IS biological. Effect is lifelong.
Hermaphrodites / intersex people are born with whatever body and sex but are chromosomally not XX or XY. They are a third sex (3rd sex, not gender). Basis is biological. Effect is lifelong.
Homosexuality is not a less-aggravated form of transgenderism. The person feels comfortable in their body and feel like normal persons of their sex who are just attracted to the members with their own sexual features. People can very rarely shift from homo to straight, although it is very rare, it does happen. Basis is probably biological because trying to force someone to change their orientation has never worked. But natural change back to straightness is also possible so it may be biological but its necessarily needn't be from birth itself. The basis on which straight person changing into a homo(if it can really happen) is doubtful though, since as before, changing someone's orientation forcefully never worked other than when it happened automatically as a result of ''straightening out'', and I haven't read anything on the opposite happening.
So a M-F transsexual undergoes castration and (estrogen)hormone therapy to make her body match her brain. But this person cannot have a full set of female sex organs transplanted into them, and are hence incapable of direct reproduction.
An F-M transsexual undergoes (testosterone)hormone therapy but may retain female reproductive organs. Again, to make the body as similar to the brain as possible. They are incapable of male reproductive functions.
So if someone wants to classify persons based on reproductive roles, and and they see transsexual persons as as incapable of it (which is true), then how is that person ''transphobic'' is he /she is only speaking the truth?
First, there is a mistake in the very first sentence. Gender (and in particular, gender identity) is not another term for sexual orientation. The way to think of it, as I have read elsewhere, is that sexual orientation is who you want to go to bed *with*, while gender identity is who you want to go to bed *as*.
Second, some intersex people do have XX or XY chromosome configurations. In fact, there has even been a case of an XY person becoming pregnant and even giving birth (to an XY daughter, incidentally):
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2190741/
It's also worth noting that not all cells in a person's body will necessary have the same genes. (In the case above, apparently some of her cells are 45,X.)
Third, never say never in terms of reproductive functions. (Actually, never say never is a good rule in biology, and even science as a whole, in general.) There has been some research suggesting that transplanting a womb into someone born with male anatomy may be possible.
As for your final question, the problem is that classifying people by their reproductive roles is rarely necessary, and it invalidates the identites of those who can't reproduce.