I think that is kind of the point. The out-of-place x, by its very incongruousness, calls attention to and centers the LGBTQ constituent. You see it even with English words of Germanic origin, like spelling "folks" as "folx" or "women" as "womxn".
Nitpick: This may be true of “folx” and “Latinx”, but “womxn” (despite sometimes-similar connotations) seems to have originated as a way to highlight/signal feminism, and has only acquired queer connotations recently.
I'm aware of the form "womyn" from the 90s, but "womxn" appears to be more recent, and differentiated from "womyn" by its explicit inclusion of trans women and woman-like nonbinary people.
Edit: Wikipedia traces "womxn" back to the 1970s, but it seems unlike "womyn" it didn't get much currency in ordinary feminist usage, only finding purchase when the queer angle was added.
