Why is Rin in a box with a roll of colored toilet paper?

Because it made her more perfect.

Jap in the box!

That would be a berserker-sized roll of TP. Not that I can really identify what it is. Material for a dress? Reminds me a Union Jack design, but there's a couple yards of it.

it's a union jack toilet paper, so you can wipe off with a silly accent

Both the English voices of Shinku (Rozen Maiden) and Rin Tohsaka are voiced by the same person, so that would give some idea to this.

But... this actually happened, I mean, as in the game, I kind of doubt Type Moon would go as far as put a Seiyuu Joke in their games

Rin in a bi--oh, wait, wrong game.

xkcd said:
Rin in a bi--oh, wait, wrong game.

It still makes me grin.