encountering the odd large Pather fleet in one of your systems
This actually makes me a bit concerned - how is this going to interact with the existing trade shortage mechanics? Ever since the change to make trade shortages appear even when there wasn't an actual fleet lost, those have functioned as just a random un-mitigatable debuff that occasionally cripples important structures.
(For example, a supplies shortage can result in a planet's stability crashing as all of its defensive structures stop providing their full stability bonus. And there's nothing you can do about it - build all the military bases you like, sometimes the game just decides 'nope, you got pirated anyway'. Even if you're there - well, temporarily installing AI cores
should help, but doesn't - yes, they reduce demand, but if there's a shortage going they also magically reduce the supply too, and for a large colony, just dropping the needed number of supplies yourself is... probably not something you've got cargo room for, nevermind the expense - since, unlike AI colonies, you don't get a nice simple 'resolve shortage by selling 2000 supplies' option. )
Adding extra hostile fleets in player systems seems like it would exacerbate this.