I know a St. Olaf graduate who is a lesbian and an atheist and had no issues on either front while at St. O.
Iowa is not “solid red”. There are definite “blue” areas there. But yes, visit and check it out thoroughly if Grinnell is on the shortlist, just as you will want to check any other places of interest.
Grinnell checks every box. Very hospitable.
Macalester. My D is a sophomore there and is friends with a lot of non-binary students. Just walking around campus, one notices lots of students who are gender nonconforming. Plus it’s definitely a school where “nerdy” things are totally cool. My D just started playing D&D for the first time this year, so the school has increased her nerdy tendencies, tee hee…but seriously, the point is that she and others feel perfectly comfortable being and doing what feels right to them.
Academics are very rigorous, professors extremely caring and connected to students. Most are called by their first names by students. Great sense of community; you really get the feeling that the students love their school. Winters are mighty cold but the campus is so compact you don’t have to walk far for anything! And the surrounding neighborhood is safe, filled with great restaurants and shops, and has great public transportation.
Good luck!
Bard, Earlham, and UVM all came to mind. Very different places, but any one could be a fit.
I would give serious thought to what support/environment is necessary on each of the fronts you mentioned (both Es and gender identity.) Your kid sounds very talented and in a potentially "fragile " space.
@confusedmominny Oberlin! PM me if you have questions as my kid currently attends there. Also check out the Oberlin student blogs - they are searchable and I recollect one post about living in Science Fiction special interest housing that involved board games and capes! The blogs in general will give you a good sense of the kinds of students that attend. It is a very accepting place and a lot of my kid’s friends go by “they” for their personal pronoun.
It also has a peer advising program that assigns all first years to a peer leader that shepherds them through orientation and their first semester. It would be difficult to fall through the cracks there. I don’t know about every major but math, physics, CS, neuroscience, and creative writing are among the strengths there.
Our tour guide at Bucknell was non-binary, and they seemed happy there
Just to correct something says above. Scripps does NOT trend conservative. It is very, very liberal. Scripps or Pitzer might be great options. Mudd or Pomona would work if they fit academically and with their interests as well (my kid was a Mudder LGBTQ kid, and had a great experience). The only 5Cs college that I’d skip would be CMC. I think your kid is lucky to be coming into college at a time when their peers are pretty good at accepting and respecting gender identity differences. Colleges are working hard to support this as well, especially most of the schools listed on this thread. I think your kid will have good options based on your description of them. 
Oh, and my kid was a physics major at Mudd with a love of literature, which she was able to feed at the other 5Cs while still getting a great physics education and research experience.
My D is a math major at St Olaf. A number in her friend group are non-binary, at least one trans, and a number also lesbian. Seems open and welcoming. Multiple D&D groups on campus–like everywhere is seems. The math department is one of the largest for a small liberal arts college. Very active department and a great Olaf-only interim study-abroad program in number theory in Budapest (this is separate from the semester long one).
Also look at Colorado College. It’s on the block plan, so 1 class at a time, and the vibe is quirky and very accepting.
However, its academic strengths are limited (arts, some humanities, and psychology), and many other areas (including math and physics mentioned by the OP) have limited offerings.
Ithaca
On campus at Colorado College may be accepting, but the surrounding community is pretty conservative.