First, another reason why it is a mystery- countries that have huge fridges usually also buy in bulk, which is very rare in Japan where most household shopping is done on a bike and Costco type shops have never really taken off.
My latest conclusion is that it’s partly to make up for the lack of convenient shelf and cupboard space in the average Japanese kitchen, leading to telling my mother in law that it shouldn’t go in the fridge (Marmite! Shortbread!) leading to complete mystery as to where to put it.
Although I have seen similar things in other Japanese houses, I am perfectly aware that most of my insight into Japan comes from one not especially typical family, so others’ ideas very gratefully received. My previous attempt to explain this is part of Japanese Gadgets and Technology Explained