Ron's disguise in the book 7 Gringrotts break-in was a transfiguration (as contrasted to the polyjuice used by Hermoine), and explicitly removed by Thief's Downfall. It's not clear that Rational!Harry's transfiguration operates by the same rules as conventional ones, and could have been stored in some way to protect against exposure, but this provides both narrative and practical evidence against the theory.

I expect that point of the pen is to demonstrate to Lord Malfoy that a) Harry is a man of his word, and thus his words are worth examining, and b) Harry is a man of /exactly/ his word, and thus worth respecting.