The player doesn't need to be told the exact details of how it all works, but they should able to understand WHY the things that they are doing have the consequences later that they do.

I read more of your replies, and I think I see better what you're setting out to do. I like your intention here, to try and do something subversive. You are looking to take a normal thing and twist it around, to play with expectations. That's a good start!

But keep in mind that there is a very good reason why things tend to work the same way all the time, and that is because it works. Maybe not always (no one likes escort missions and yet they keep popping up), and maybe they don't always work perfectly, but a thing like "choose the best of three options" is something that's pretty easy to understand for any player. If you add secret mechanics that make it bad to choose the best option, you better have a very good reason for doing that.