Alrighty, I double checked with the development team. As everyone has been mentioning, currently automatons cannot cast Protect and Shell on themselves, but the team is looking into making this possible. I'll keep you posted once there is more information. Apologies again about the confusion!

Additionally, I have some other information regarding puppetmaster to share.
  • Automaton weapon skill adjustments
    We’ll be making adjustments to automaton weapon skills in the August version update to increase the value of being able to fight alongside your automaton.

  • Target Marker adjustments
    Previously we received reports that the Target Marker was not functioning properly while in high-tier mission battlefields, and we’ve confirmed the issue. The team is currently looking into how to address this. There is a possibility that the way the Target Marker functions will be heavily changed. (However, we’ll be careful not to make it so the stats are reduced.)

  • Tactical Processor adjustments
    Coinciding with the aforementioned Target Marker adjustments we will also be making long awaited adjustments to the Tactical Processor.