Most feminism is going to end up being at least somewhat focused on cis women specifically in some way or another, just because cis women make up the vast majority of women. That's not necessarily transphobic, just an unfortunate side effect of something like 99% of women having certain specific traits that something like 99% of non-women don't have. Often it's just negligence, if that's the right word, rather than malice.

I'm no scholar of feminism but I feel like the push to be gender neutral about absolutely everything is in many ways harmful to feminism and often ends up doing more harm than good. Also, unfortunately, often pushes people neutral on trans issues towards being more transphobic. Bad optics, you know? Screeching at a feminist that she's transphobic and making a huge fuss about it because she's using a pussy to represent feminism is probably only going to piss her off and make her like trans people less, it's probably not going to make her think "Oh true I should be more considerate of trans women". People often just can't be polite about these kinds of things and jump straight to making everything a vitriolic fight. It's also easy to end up feeling like it's just more suppression of speech and self expression. It's a complicated issue.