I've also complained about this as it's not transparent how you should go about actually owning and managing an automated fleet.
I was surprised that the automated skill AND an alpha core (embedded into a single radiant) is barely enough to raise the CR to 50%
Impossible to also have multiple automated ships as they destroy the CR, so an otherwise fun mechanic is seriously limited, not fun imo.
Because honestly capturing strong autonomous ships is tricky and trying to get a core from a Nexus is also hard, unless you already have a strong fleet.