The amount of time matters. The 5 hours required for solar disinfecting is far less than the time a plastic bottle will degrade in the sun and contaminate the contained liquids.

Polyethylene terephthalate (PET - commonly used for soda bottles) can withstand direct sunlight for 5 years. There's leeching occurring throughout the degradation, and I can't find any trustworthy research on leeched PET harm when ingested repeatedly over a lifetime, but a few hours in the sun is pretty far from the danger zone.

All things equal, I'd rather deal with a small risk associated with pollutants leeching from the bottle, than the much higher risk associated with diarrhea-causing organisms in the water.