So Uncanny agility states:
You are immune to the flat-footed condition, and your opponent doesn’t gain any bonuses to attack rolls against you from flanking you or attacking you when you’re prone. Furthermore, covering fire and harrying fire don’t provide any advantage against you.
You are lying on the ground. You take a –4 penalty to melee attack rolls. You gain a +4 bonus to your Armor Class against ranged attacks, but you take a –4 penalty to your Armor Class against melee attacks. Standing up from prone is a move action.
It seems that with RAW operatives would still get -4 penalty to attack rolls and AC as those are not bonuses to attack rolls against the operative. Or is uncanny agility covering something else?
I think the spirit of the rule would be that the operative would get no negative at least to their AC.