Tempurature. This is because if it is in any other container, it could absorb the sun's heat, making the milk warmer. With the clear bottle, the sun's heat will mostly pass through it.
Milk sold in clear bottles might be low in Riboflavin
Riboflavin is a sort of vitamin that could be commonly found in dairy products that has a function to prevent migrain. The thing is, Riboflavin is a temperature sensitive substance and could be easily destroyed by heat or exposure to light
