I was stumped by this too for a while, but then I figured it out.

Freelancer physical components
First off, these components should NOT be in Stanton shops. You should not be able to purchase military components at all, and the only reason CIG has so far allowed us to is because... they had nowhere else to put them.
So the PVE Bobs begin from false premises. Even if putting these components in Pyro makes no sense, it makes as little sense to offer them in Stanton shops.
But where should you be able to acquire military components anyway?
Only one way: in the black market, from criminals.
And where do criminals live?
In Pyro.
So it makes perfect sense for CIG to put the components there.
As for where the criminals get the components from... they get them from military bases. So players could skip the middleman and try to break into those bases. But where are those bases located? Not in Stanton. It's a megacorp-owned system, while Pyro is not part of the UEE at all. Nor is Nyx, the next (lawless) system to be introduced. But after that comes Castra, which used to be a weapons-testing system. So there should be bases there for us to infiltrate.
Until then, there's Pyro. (Weapons factories are another possible source, and those SHOULD exist in Stanton, but don't currently. So this is what the PVE Bobs should be asking for: Physicalized weapons factories in Stanton.)
So we see Supreme Commander recoil's mission list grow as CIG crams more and more valuable assets into Pyro, as now on top of everything else he has to build up a strategic reserve of high-end components in Pyro, and then help upgrade The Cult's fleets with them, and I have amended the text of his orders to reflect that [ > ].
For more info on how components work, consult: https://starcitizen.tools/Ship_components
- Grade A - The best possible performance, usually has an additional Sub Item slot.
- Grade B - A good upgrade to performance, may have an additional Sub item slot.
- Grade C - The standard item for most ships be default, average performance.
- Grade D - Lower grade, generally makes up the NPC/AI populace, good for emergency use to get through troubles.
- Military - The best overall at that item's functionality, at the expense of emissions and cost.
- Civilian - The most common, wide range of behaviours to suit cost, options to approximate all other categories but not as specific.
- Stealth - Vastly reduced signatures/consumption at the expense of functionality.
- Industrial - Reliably high output and low wear, high emissions.
- Competition - Higher performing than military but at the expense of durability and stealth, performance over everything.
These mechanics are still under development and may change in future, but for now the above details are a good start. In short, we need these components, and it's Supreme Commander recoil's job to get them for us.
It may also be possible to purchase them from players, and we'll look into that too. But that's not recoil's job. That's the job of the heads of the three Noble Houses back in Stanton. recoil's job, and the job of his followers, is to steal as many of these components as they can, and store them safely for the rest of The Cult to access and use.