NPR may not align with MSNBC on everything, but it certainly does take sides on culture-war issues.
NPR very consistently refers to sex-change operations or hormone treatments as "gender-affirming care," a phrase which on its face, makes a judgment about whether these medical procedures and treatments are a good idea. Whatever your opinion, the phrase is an expression of an opinion on this hot topic.
Similarly, NPR routinely uses gender-ambiguous pronouns, and often refers to "pregnant people"--both editorial choices that make a statement about their opinion on gender identity issues.
The same slant is seen when discussing hot topics like the renaming of teams and mascots tied to native Americans, or student loan forgiveness, or the role of the Federal government in education.