Dissonance in seventh and extended chords

I have two problems with using seventh and extended chords (with current sus4/sus2 system) in Hookpad:

  1. Inverted major seventh chords create sharp dissonance, as major sevenths become minor seconds;
  2. Perfect fifths in extended chords often clash with melody note, again creating dissonant minor seconds.

Should there be a way to specify which notes are to be omitted/doubled and how the notes are arranged in a chord?

No, because afaik Hookpad is not for designing voice leading; although it can algorithmically turn minor seconds in the generated chord voicing into major sevenths.