It's just dawned on me why the IDs are wrong. Eloquent will be using FETCH_ASSOC internally, and due to the query doing "select *" there will be collisions on the id field.

Altering the PHP as follows fixes it,

$results = TableA::with('tableB')
      ->join('tableABPivot', 'tableABPivot.candidate_id', '=', 'tableA.id')
      ->join('tableB', 'tableB.id', '=', 'tableABPivot.election_id')
      ->where('tableA.visible', 1)
      ->where('tableA.first_name', '<>', '')
      ->where('tableA.last_name', '<>', '')
      ->whereIn('tableA.affiliation_id', [100, 200])
      ->where('tableB.scope', 'value1')
      ->whereIn('tableB.rating', [4, 5, 6])
      ->where('tableB.type', '<>', 'value2')
      ->orderBy('tableA.last_name', 'ASC')
      ->take(100)
      ->get(['tableA.*']);

Note the alteration to get().

Thank you forum for being my rubber duck.