I don't know the actual answer - if there is one. I always thought they were just different colours so you could identify what type/weight of thread you had on them. So you could use pink for say ordinary sewing thread, blue for say embroidery thread, and clear for bobbin thread - just my thoughts.
Having different colour bobbins is one of the reasons - apart from price - that I ordered 3 lots of 25 from China in great bobbin boxes (about £2 or £3 with postage each). Each box has 5 different colours. There are only a couple which are a bit tight over the bobbin winding spindle, but I haven't found any issues at all in using any of them.
"Live like someone left the gate open". Kimberly Burnham