hi, ray. If you apply MEXT scholarship through university recommendation in two universtities, it's clearly stated that if you do that, you will be automatically disqualified.
Actually, if you apply, the university will begin to selected people and only a certain number of ppls among the applicants will be recommended to the MEXT. You can maximize your chance of getting the scholarship by applying for two at the same time (though it's not allowed, the two universities themselves wouldn't know that you have applied for two universities), then after the university selection, you should ask your professors if you will be recommended to MEXT by the university, if both universities will recommend you, then you must immediately turn one down as soon as possible, before they both hand your materials to MEXT. If only one university will recommend you, then it's just as good as you have only applied for one university. You know what I mean. The universities wouldn't send the materials of those that they don't recommend to MEXT.
However, that's only my guess. Think about it very hard yourself before you really want to apply the MEXT university recommendation at two universities at the same time.