(It's not story-related, so I'm unspoiling.)Will the reason for this become apparent later in the story? Is this how Janet's mind works?
On a meta-level, it's how the player's mind works. Playing through a branching-plot game is about weaving your way through a maze of possibilities and trying to forge a connection from your start point to the ending you hope for.
At one point in design there was going to be a framing story in which you-the-player have received a mysterious puzzlebox on which you are watching Janet's story take place like a movie. (See all the strange metallic tubes and gears around the viewscreen?) Therefore your adjustments to the box's wiring change the way that the story inside plays out. (You may notice, for example, that the choice puzzles always ask "What does JANET do?" rather than "What do YOU do?") But making this framing story explicit really didn't add anything to the game so it faded away.
As for why, two real reasons... I personally like having a minigame break from reading every now and then when playing VNs, and I'd been reading a discussion of gameplay vs story segregation with regards to a particular casual game. It had both gameplay elements and a plot with decisions to make, but the two were totally separate. You played the game section and then you made an explicit choice afterwards, and the blogger mused about how it might be nice to make choices via gameplay. So I set about making "the act of choosing" into a game element (Well, I designed a way for it to BE a game element - the Caterpillar CODED it, obviously.
)Having to work towards the goal you want to choose adds a little bit of weight to the decision.
Though the endings make up for it~ The one I got was sad DX
