Interesting.Hi Magaji. You would need to clarify at your school at which stage your application process is. The content of the emails is simply congratulations, etc., I had to clarify from my school what it meant each time. So for me it was three emails. First congratulations email came from my graduate school, turns out it is just nomination by the graduate school within university (not actually nominating to MEXT). After that one you may have had an interview. Second congratulating email was about nominating from the university level (higher level from your graduate school). And then there was a third congratulations email, which meant confirmation from MEXT. So, just ask your school directly, the wording in those emails can be ambiguous. Good luck!
The email from my university was rather clear, I was selected by the university and I will be recommended to MEXT after filling the pledge form and MEXT updated form.
The final confirmation from MEXT traditionally comes in May, June or July depending on the program. That's why i wondered when you got your confirmation email this March, perhaps MEXT is changing it's timeline.