I feel like @Neitsa answered my question in their comment to the original post. I'll quote it here.
But be wary that PIN starts very early in the process life, so it starts instrumenting everything the system loader is doing (basically in the libc). The fact that you have two different instruction count is probably due to a if / else branch somewhere in the ELF loading code (depending of the system state at a 't' time). If this bothers you you can restrict the instrumentation code to your own binary if you wish.