In the “Piano” instrument setting for the harmony track, Hookpad uses a 3-note right hand (RH) voicing assuming that the piano bass track will be defining the inversion. If you import the bass track you’ll see that the proper note is on the bottom.
We do this for a couple reasons. First, this is similar to the way that a real piano player would play this progression, using the left hand to define the inversions and the right hand to fill in the rest of the chord. Second, if you voice the harmony track with the bass note at the bottom of the right hand, then you will essentially have parallel motion between the right hand chords and the left hand bass. This tends to sound super awkward in playback, which usually is what you’re most concerned with when exporting MIDI to your DAW. In other words, when creating a rhythm section, backup strings, etc, you typically don’t want the bass note at the bottom of your chord for your mid-range instruments.
One way around this would to have Hookpad voice open position chords. We actually do this presently for some string and pad instruments. This doesn’t fix the parallel octave problem, but it does serve to make certain instruments feel more ambient (depending on their timbre). After a lot of experimenting though, we found that we liked the closed position piano chords the best.
When I use Hookpad MIDI files in Logic, I usually just create one track for the right hand and one track for the bass, or I merge the two MIDI regions together. In the next version of Hookpad we’re considering grouping similar instruments into the same tracks, since I find that’s what I’m usually looking for. Thanks for your understanding.