That is the remnant of one of the attachments between the Command and Service modules (there were three). Here is a cutaway drawing showing the bolt penetrating the heat shield (labeled "tension tie").
From Apollo Experience Report Spacecraft Structure Subsystem
Here's a closer picture showing that the circular areas are not penetrations but worn spots where the command module rested on the support structure.
The bolts, support structure, and circular pads can be seen in this drawing from the Apollo Spacecraft News Reference (annotations mine)
