The one you're talking about is MEXT for undergrad, which you can't sign up for if you already have a BS.
Mext for research students+ doesn't really care about what field you choose to pursue. You can do your master's in a different field, though you might have to explain why at the interview. The MEXT exam is English and Japanese only, no prep year (you can do a 6 months japanese course at your uni, but it won't be the amazing intense one year course that actually teaches you japanese, and you will be expected to do your reesearch regardless). You can sign up for prpgrammes in English.
Mext for research students+ doesn't really care about what field you choose to pursue. You can do your master's in a different field, though you might have to explain why at the interview. The MEXT exam is English and Japanese only, no prep year (you can do a 6 months japanese course at your uni, but it won't be the amazing intense one year course that actually teaches you japanese, and you will be expected to do your reesearch regardless). You can sign up for prpgrammes in English.