Box -Hako-: Story
Supposedly, the main character is the Ultra-man of that planet, and the supposed 'mini-sized' girls are actually in the NORMAL size of the residents of that planet.
It's not that they are small, but HE is the one which is over-sized...The house which the game takes place in, is actually an over-sized building the government built for the main character to live in, and in return he helps them fight the monsters which invade their planet.
The 'Box-Girls', which to us the players may have seemed to be just a new line of pets product or something, takes on yet another meaning, now that we realize that they are of the same size as the rest of the population on the planet.
Young females, who automatically generate themselves just by being placed inside a special container, and can be steadily MANUFACTURED, who are basically affectionate to the owner since the first time he opens the door to her 'room', and automatically degenerates out of existence by the end of a few days.
Oh no, they are not trying to make 'pets'. They are trying to make Automatic-self-disposal SEX SLAVES.
However, the true sizes of the characters are not revealed until the very end of the game. In fact it is portrayed as if it the girls are the small ones, as it can be seen in various CG's. Some are the view from the characters apartment, the postman supposingly delivering the boxes through a large mailbox ect, which strongly suggests that it is the girls which are small.
There is a possibility that there may be other Ultra-Humans existing on the planet, due to the main character often receives Emails from people discussing about their own Hako Girls and how they should take care of them. Unfortunately this contradicts the theory of the marketing of the Hako Girls, due to having little amount of customers the size of the main character. The normal residents don't seem to purchase such Girls, since the emails often suggest that the girls live in the boxes, and that the customers do things that they possibly couldn't do if normal sized, like feeding the girls impossibly huge manufactured food items.
Illusion possibly implemented the large plot twist at the end, mainly to throw the players off guard.