Heretic or Phantom
 

I am curious as to the consequences of choosing one over the other, from what I gathered, I do know that giving the cargo to Heretic will later get you the Pirate loot mission, wheras giving the cargo to Phantom will later get you the USS cargo mission in Debris, but given the difficulty and underwhelming reward (30000 on hard difficulty, a drop in the bucket compared to the oodles and oodles of loot in Pegasus), and the fact there is a completely random encounter with Phantom if you go the Mercenary (NESF) route, makes me believe that there must be some other bonus, but I have not gotten that far in my new game yet.

just finished the Pegasus 5 min ago.

Well, I got 1 G4(Trident) and 1 heavy machinegun(reloaded 3 times, exactly the same loot), that is all,
while spend 25k credit for hiring Mechenary(if i knew there is a station at the destination, would save 5k on mech jumping cost.
But I got 1 extra mother ship turrent and radar(300km), and most improtantly, a lot of exp in early stage.

and what is the "USS cargo mission in Debris"
is that the fake cargo delivery?

Yeah, same mission...

Anyhow, I just got to the random event in the Merc system, and Phantom just gives me 25K and a word in with Corsair, but it does not seem to affect the NESF mission line in any significant way (although the dialogues are slightly different)...

So all in all I get 55K total.... not worth it at all.

I set the cargo drop to 100%, so I get all that a cache contains. If you want to reload a cache, you have to exit and re-enter the system.

From the Paymaster's loot alone, I got a repair system, a shield system, some turrets and a major caliber gun... worth a couple million easily.

Not only this, though, the mission also spawns about a half dozen 'stashroids' that you can blow up for even more goodies.

Reloading for a new drop
 

You dont need to reload to have a new drop. Its just about patience to reload some more times to get another loot.

The thing is, there are two calculations going on here...

Calculation 1 occurs when the Paymaster and his convoy spawn. The only way you can change this is by reloading a save from before the Paymaster spawns.

Calculation 2 occurs when the ships are destroyed. This is a percentage calculation, basically, X percent of cargo is destroyed. In my particular game, I set the cargo to drop 100% of the time, which means I get the full cargo.

The Paymaster's loot probably saved me about several million in mothership upgrades (Kali and Aegis shield gens, Smog antimissile, Quasar sensor, and some others, no repair system unfortunately), and I got about a hundred thousand from extra mothership components (Sold a Fog antimissile and a Paralaxx sensor suite)

what does Calculation 1 do again?

That is the code.

Basically, it spawns a random amount of loot from the shipmodulesrare directory into the transport's inventory.