Nall-ohki, congrats. We may be able to meet up depending on where you go.
Menrui- from the application guidelines
If a candidate grantee has received a letter of provisional acceptance from a university, first of all MEXT will request the university to receive the grantee, and place him/her there upon its approval. If a candidate wants to enter a public or private university, the grantee's preference may not be met due to budgetary reasons concerning school fees, etc.
If a candidate has obtained neither admission nor a letter of provisional acceptance, MEXT will contact related universities and decide at which university to place the candidate in consideration of his/her preference. In this case, the candidate is not allowed to raise an objection to the decision. In a case where a candidate fails to obtain admission or a letter of acceptance and MEXT discusses the case with related universities, the candidate may not be accepted and therefore not definitively selected by MEXT, if his/her research program is vague or unclear, the content of his/her research is not substantial, or his/her desired major field presents difficulty from the perspective of research guidance.
From my consulate,
In the case that you receive a couple of ツ"Letter of Acceptance,ツ" MEXT will firstly contact your first choice university. If the university refuses to accept you (because of lack of budget etc), then MEXT will contact your second-choice university. Therefore, you need to clearly state your preferences in order at 7. iii) of the ツ"Attachment.ツ"
I think that the embassy and MEXT expect that some candidates will have received multiple LoA's, thus the space for 3 universities on the ranking sheet.