currently the base userland is not controlled by the pkg system. You can use freebsd-update to do a binary upgrade, which will also sync your kernel sources if you have stuff in /usr/src, so you can simply rebuild kernel after running the update.
Should be noted in 11-CURRENT there is currently ongoing work to move userland and the generic kernel into pkg, so look forward to that as well.
Maybe there was a time it was using the old kmod port?