From my own experience, if you were to embark with semi-intelligent pets, they act as hybrid citizens committing to both behaviors, taking trolls as a prime example which are selectable by [EVIL] civs.
> Trolls occupy spare citizen room & can work at occupations indiscriminately & also be drafted into the army
> There is no way to personally identify who a troll *full title - "Troll (Tame)"* is and they will breed like animals through close contact, this makes keeping track of trolls in the army quite difficult.
> Trolls are treated like livestock, but much of the UI is bugged to not recognise this, for instance you have to hotkey (s) on the preferences screen to have them slaughtered, and the goods are *via bugs* unsuable.
Its actually quite bugged and inconsistent at the moment because its largely unintentional.
I have some indepth suggestions how to improve here, but otherwise the only things i can prescribe modwise is to play around the issues.
> keep trolls & semi/full intelligent livestock in burrows as to handle them easier and provide access to food & a tavern to keep them busy.
> Disallow trolls/semi-intelligents from claiming rooms by micromanaging, so that they use dormitories inside the burrows instead.
> Trolls cannot independently fight in a squad (semi intelligent forbids it), they require atleast 1 intelligent squad member before disbanding.
> If you have access to a semi-intelligent (troggs/trolls etc.) bring females & breed them from males on a chain rather than mod them in to be tamable, as its much more natural and less messy.