The fingering for arpeggios is just for that - arpeggios and block chords. Whichever fingers get used will depend, to an extent, on who's playing them, due to hand size, dexterity, etc.
In order to play the melody over chords, using the same hand, will, of course, necessitate having a free finger (or two) to do just that, and it makes sense that it's pinky (and sometimes ring) that come into play there.
So, the two things are slightly divorced from each other, as each has a separate function. But it's the usual way we add 6ths, 7ths etc., to standard shaped chords anyway - it's what guitarists have always done. (Just comparing the same situation with another instrument).
When playing a melody, the highest notes are usually the ones perceived to be that melody, and since pinky is situated there, that's what gets used. It's often the weakest finger, so extra practice will be needed to make that melody sing out, but it's worth the effort. It will also, at times, be expected to stretch further than its usual distance when playing arpeggios or 'normal' chords, so examining what notes can be played underneath by the remaining fingers is paramount. Keep going with it!