You could probably use InnoDB for everything, but the idea of some usage of MyISAM is that in theory MyISAM is faster when you don't need the more advanced features of InnoDB. Search the internet for:
"MyISAM vs InnoDB"
"When is MyISAM better than InnoDB"
"When is InnoDB better than MyISAM"
I'm not a database guru, so I could be persuaded to change these in the repo if somebody that is truly qualified told me I was doing it wrong.