Updated via app store.
Rebooted without using nv_disable=1 flag and osX told me it was using the default driver so I installed the new Nvidia driver, rebooted and all was back to normal.
So it should now be possible to update without using the nv_disable=1 boot flag.
Tried to update last night. It downloaded, started installing, and froze at the apple logo and progress bar saying "Time Remaining: 12 minutes". Sat there for 30 minutes until I forced a restart. It booted up fine with no issues, but I'm still on 10.11.2 and it's asking to restart to install. I'll try the update again tonight and if it doesn't work from the App Store, I'll use the combo update dmg.
Update: Ran the update from the App Store again and it ran smoothly. Rebooted and Nvidia alerted me to download the new drivers, rebooted again and all is well including iMessage and audio.