Gender alignment has two meanings.
A. Gender alignment is terminology used by some nonbinary people to describe their experience of gender. For instance, a genderless person may identify as female-aligned because they have experiences in common with women, or a demiboy may identify as male-aligned because they are partly a boy, or a maverique may identify as unaligned because they have no ties to manhood or womanhood.
The meaning of alignment terminology differs from person to person. Mod Lune on the tumblr blog We Don't Care About Your Binary put it this way:
|«||Some people use (wo)man-aligned to mean “the social category I belong to is (wo)men”.
Some people use it to mean “I present as a (wo)man.”
Some people use it to mean “I am read by other people as a (wo)man.”
Some people use it to mean “my gender is somehow, in some way, related to (wo)manhood.”
Some people use it to mean “I am closeted and outwardly identify as a (wo)man.”
Some people use it to mean “I experience queer sexuality like a (wo)man.”
Some people use it to mean “I interact with patriarchy like a (wo)man.”
B. The term gender alignment is also used to describe a person's status as cis, trans, or nonbinary (As in "does their assigned gender at birth align with their gender identity or not?"), for example in the phrase Marginalized Orientations, Gender Alignments, and Intersex.