Stopping or transiting at Iquique? SCL-IQQ-LPB is using the same flight number unless something has changed lately so I would imagine that it can count as one or two segments depending on the routing.

Are you just transiting at Lima? I'm asking this as it's very common to visit Cusco Machu Picchu, Sacred Valley etc) and Puno (Lake Titicaca). Both cities are much closer to La Paz and surface sector between La Paz and Juliaca (closest airport to Puno) or Cuzco would make more sense than to fly Cusco/Juliaca (Puno) via Lima.