@CorsairZero
I'll probably make it so they explain that pirates have encrypted signals even with their transponder off along with a warning to leave them alone, and give the player a pass (if the player passes a cargo scan) if they have a commission. The player will still have to keep their transponder on, however. There are technical reasons for this mostly.
I'll probably also make the pirates at Mordreath neutral once the player takes a commission with the AC.
1. The change for Pirates being (more or less) neutral to AC-commissioned fleets in AC space seems tentatively reasonable.
2. I would prefer you not to implement the free pass for passing a cargo scan with AC fleets, outside of the high rep mechanics consistent with other civilized factions. If it's illegal to have my transponder off in AC space, then I should be punished for getting caught with my transponder off in AC space.
3. I don't love the band-aid/hand-wave fix of encryption lore, but to be fair I have almost the same issue with vanilla NPC smugglers getting free passes from most/all civilized/law-enforcing factions. I dislike double standards, primarily (maybe even exclusively) when it's unjustifiable/unbelievable. I attribute the smuggler issue to dev oversight or, more charitably, to "it's in alpha".
But color me, a questionable leader incapable of growing any of my colony's populations above about half of what the NPC factions are capable of, or only being able to be competitively and logistically efficient when dealing with <3001 units of both cargo and fuel, displeased.
Moving back from that digression:
The (corrupt) act of looking the other way for a high rep character or a special case such as the PC not having to obey the transponder law in part of the tutorial? Both good by me. Both believable.
(Assuming this is different than the Pirates labeled as "Scavenger") Pirate transponder modifications that are only available to Pirates (in Mordreath), utilized consistently by all Pirates in Mordreath, that are also going to be so well made by the same engineers/workers making/maintaining the Pirate's jury-rigged fleets that they could fool AC fleets at close range? No dice.