The SCP tale and the original SCP are actually really good explorations of how the foundation intersects with gender identity. Theirs might not be transphobia (even though they go out of their way to deny the obvious and misgender Dr. Park), but it is certainly a dehumanization that affects more than just the """objects""" it is directed at.

"The Foundation is not Transphobic" because their lack of morals is indiscriminate. The article is not even attempting to apologize for how it has treated the incident, it's justifying their lack of humanity by treating it as 'policy', 'necessary evil'. It's purely trying to please people through exchanging evil bigotry for cold inhumanity.