Yes the BLM and RNG automations are squishy and for reason. Just like the counterparts, the design is for dmg, and the more dmg you do, the more squishy you are, in most cases. If a pld could out DD everyone, while having the best defense why play anything else. Probably the same idea there.
You can definitely buff them to be more durable but you lose dmg.
You really have to pick your automation for the mob. If you fighting a AOE mob that will reach past your automations damage range, bring out VE.
I think many pups like to just use one puppet and don't adjust to the situation.