Not to toot our horn, but both our daughters chose the 理系 track in high school, and went on to science in uni. The older one did miss and took a year to study before taking the exams again, but then did applied chem at Osaka. And after graduation was able to stay on the technical side of things in the job she got, working on some simulations which involved a lot of computer work, then later (after childcare leave) was able to get into something different, building an app or two used internally in the company.
The younger one was always a whiz, and tested into the 2nd department of science at U-tokyo. After that, which included a year abroad, she went to the states, worked as a lab assistant for a couple years (something connected to RNA and grinding up fruit flies), and then entered grad school. She'll be done with that a year from now (if everything goes right), a little more if her advisors get picky. Phd in bioinformatics..., big data as used in medicine. She doesn't do any "wet lab" work, it's apparently all stats, python, R, and so on, but also working with people to get projects done. Tho she hasn't closed the door on returning to japan, I think she'll be staying in the US to work, probably some pharma/biotech job.
The older one was lucky, in that her husband was seconded to california, so she has, after taking care of their kids' daycare and now 1st grade there for the older one, been looking at work and interviewing. She did work briefly for a branch of Itochu last winter, but the company didn't suit her. Their stay there is not permanent, maybe a few more years, and I hope she is able to assemble a path and some experience that will lead to something satisfying that she can do here when they get back--either in person here, or remote, something like that.
But yeah, I don't think 'the system' here in japan (even tho it had a strong hand in producing them) is really set up to take advantage of and utilize these kinds of people/women.