In the MISJ, romanization is used in the beginning to give you some hints of Japanese sounds until you learn all the "HILAGANA" and "KATAKANA". However, it is gradually removed as the lessons go on.
Since they are treated as temporary tools, I tried to be as honest as possible to the Japanese sound system. So, some of the usage of the alphabet is slightly different from the romanizaton which you will ordinarily find in other textbooks.