Punctuation aside (and yes, there's a lot of mistakes, run-ons, etc.)...
This is a pretty good piece for discussion. I believe the symbolism that Nero is referring to is the fact that the author is speaking with regard to MtF pre-op or non-op individual who retain (temporarily or permanently) their "penis," "Phallus," or whatever they wish to call it.
The author makes some good points, but they are making a lot of generalizations with regard to the transwoman's body. The transwoman's penis (or any penis) is not inherently a weapon to be used against anyone, though it can be. The penis is not an evil symbol of patriarchy and male dominance, it is simply (in the case of the MtF) a deformity which can be corrected if she so chooses.
In short, the penis is simply flesh and blood; an organ designed for pleasure and procreation. How one decides to use that organ, is up to them, and that individual alone is responsible for the consequences of such use. That does not make all penis' inherently evil or somehow construe them as misogynistic symbols of the patriarchy.
Before transition, her penis, symbolizing patriarchial violence and sexism, symbolizes her body as dangerous and unsafe, threatening to women–including her.
The penis does not represent nor symbolize patriarchal violence or sexism; these are social constructs that were created, not by the penis, but by individual men over time. I majored in Women's Studies in college...Personally, I think this article is transphobic, and is as damaging to the MtF individual as radical feminism's views on transgendered people in general (think Michigan's Womyn's Music Festival's policies on "only womyn-born-womyn may enter."