What a lively discussion.
I typically only do this level of micro-management on harder targets (Mk.IV+). Send X units to attack a guard post, send Y units to hit a different guard post, retreat before angering the AI and wiping a fleet. Rebuild, re-deploy, rinse and repeat until the planet is whittled down.
As for ship-line-level standing orders, I'm neutral. I think it'd be nice for some niche circumstances, though I'm not sure if those niche situations warrant the development time required to implement the change. I can understand the need to keep X unit out of the way, or have Y unit in group-move while the rest freely move about as they please (Swarm-style units). And I'm sympathetic to those who find the custom flagships a bit clunky to use for this use case. So, I'm on the fence.
That said, though, if custom flagships are the solution to this issue, I'd like to draw attention to this change from the upcoming 1.004 patch:
Eyes can now be triggered by the number of fleets on a planet, not just the number of ships
If using more fleets is the method we should use to gain more granular control over ship behavior and standing orders, it seems counter-intuitive to have a mechanic in place that penalizes using that method. I understand the change's purpose, but if I'm organizing ships into multiple smaller fleets to gain the level of control I want, then I could very well trigger an AI eye purely because I've organized my forces more than the AI would prefer. Or, put differently, I could have 100 ships and not trigger the eye with 1 fleet, but organizing those 100 ships into 3 fleets could then trigger it. I wholeheartedly agree with the spirit of this change (prevent the player from stacking loads of low-unit-cap fleets to circumvent the eye mechanics), but this is a situation where I feel like two ideas about how the game should work collide.
All of that out of the way, I'm still a newbie, here, so take my $0.02 with a hefty amount of salt.