Scripps has been accepting trans applicants since 2014 Scripps Approves Trans-Inclusive Admissions Policy | The Student Life It also isn’t uncommon for students to transition once on campus. My daughter’s graduating class included a trans man and an unknown but definitely nonzero number of nonbinary graduates. The campus life of the five Claremont Colleges is so blended that all gender identities are well represented in daily life. The Queer Resource Center serves the whole consortium and is good source of information on the nuances of housing, etc. Scripps College - Queer Resource Center at The Claremont Colleges
The 5C’s are terrific for sciences and foreign languages. CS at Mudd and Pomona is very strong too, but access to these classes and off-campus majors from Scripps has become less certain than it was in the past. (It’s still happening but the promise of unrestricted access has been rolled back a bit, and it’s unclear how this will play out in the future.) The Pomona Cognitive Science major is not restricted though, and could be a good place to combine sciences (bio/chem/neuroscience) with CS classes, particularly if your D’s interest in multiple languages also implies an interest in linguistics. (Linguistics and CogSci share a department at Pomona).
The thing is that the maximum merit at Scripps is half-tuition, which still leaves about a 50K/year cost of attendance, absolute-best-case, unless the NPC shows that need-based aid would give you a lower COA than that. MoHo does have some full-tuition merit scholarships.
URochester is another that’s strong in all your target areas and does give merit, but not getting-you-down-to-30K type merit.
I’m thinking that maybe some of the smaller New England flagship U’s would provide the kind of environment and programs you’re looking for, but closer to your price point. Maine and NH are the cheapest but I’m less confident of trans-acceptance there than at, for example, UVM. (No firsthand experience with NH or Maine on this front though, so I’d be happy to be corrected by folks who know these schools well.) URI is especially strong in its language programs, and interdisciplinary programs in FL+X. Would any of these programs appeal? https://web.uri.edu/global/globalize-your-degree/signature-international-programs/