If you want to reduce the electrical noise ('whine' or 'hash' are typical names) from an alternator, the right place to filter it is right at the terminal. They may not have had enough room inside the alternator package to make a sufficent filter, and had to add an extra cap outside to knock the noise down to the level they were seeking.
Not uncommon, given the suppression used in the MEP gensets - they typically have small value filters on each output phase. You'd never know there were there - unless you went looking for them or saw them in the TM.