Organ / Keyboard Particularities

No, this is working per the settings you have chosen on the Ties page of Engraving Options. The ties on single notes are positioned outside (above, in this case) the notehead, while the ties on chords are positioned between the noteheads. You can adjust the Engraving Options to produce a more consistent layout in this case by specifying that ties on single notes should be positioned between noteheads.