You should know by now that there are very, very few effects out there that have a reason. The reason for the trick is to entertain, do the impossible... putting a pen in a water bottle like that is pretty impossible.
I disagree with you specifically the statement that few effects have justification. If anyone lives by this I can make the presumption that you're lazy.
Entertain hmm do the impossible? Putting a pen in a bottle without presentation is just that, just differently. It looses its impossibility because it comes off as a puzzle.
Now back to my first question, does it have to be a pen or could it be a pencil, exacto knife?