Mist, I'm leaning toward your thoughts.
The piece may have been missing long before the crime was committed. I'm playing the scene through my mind and trying to figure out at what point the brush was broken and why someone would do that (either purposefully or accidentally).
I understood Meyer to mean JonBenet's injury was consistent with digital penetration. Steve Thomas said a splinter was found and the autopsy uses the terminology birefringent material. While UKGuy has stated he believes Meyer was being cryptic by saying "birefringent" to avoid saying splinter. I don't hold that opinion. Autopsies are not meant to be cryptic. They are designed to be scientifically specific. I'm sure UKGuy will correct me if I've misstated his position.
I don't know of anything that proves a portion of the paintbrush handle was used vaginally on JonBenet but maybe someone can come up with something convincing that demonstrates that possibility. I think, based on my reading, that this is theory that has taken on it's own life and become a "fact." If I remember correctly, some foreign animal hair was also found on JonBenet, maybe a couple of hairs on the exterior of her clothes (can't remember for sure right now). There's speculation that hair came from the head of one of the brushes in Patsy's paint tote.