It's the "same pen" despite the fact that in reality its physical makeup is in a constant state of change?
You seem to be saying that the concept of "the same pen" has its basis in something other than physical reality -- it's an abstract concept of the sort that Plato talked about in his theory of "forms."
No. The basis is in reality. I'm also the same person I was yesterday, even though I had some more coffee, took a few leaks and gobbled up a bag of candy bars.