Pen is unsightly and over the years it'll either fade or bleed up into the foot's plastic. It's also not a deterrent for a truly unscrupulous seller, as it can easily be sunfaded away. It can help in cases where the seller is unaware of what they have, but it won't stop someone who intends to be deceptive.
Using a scalpel to carefully carve out "RH" is potentially a better alternative, since that's a lot harder to cover up, but it's also harder to see and still is damaging to the original, which many people don't like. The paper inside method again won't stop dishonest sellers and may not be seen by honest ones, if they never think to pop the head open, which most won't. It's a conundrum.