I think that even though the submission dates for LoA differ from country to country, the date when the LoAs have to have arrived at MEXT is the same for all countries. Correct me if I'm wrong. I was told at first that I can submit my LoA by the end of September so I can take my time considering the preferences, but after getting the last LoA I was asked to submit it a bit earlier than September 30 because the LoAs had to be at MEXT by October 3.
It certainly is weird that some embassies contact the successful applicants now and some seem not to do the same. It might be different embassy procedures. I recall reading here in one of the threads on MEXT scholarship from previous years that someone was contacted first by the university in December and asked about their accommodation preferences while they still had no info about the outcome of the second screening.
Thanks Kurapan