Obviously an engineer doesn't need 5 copies of the exact same data to upgrade your module.
There is a handwave which basically makes narrative sense for the Engineering implementation (though it does break for synthesis). At least some of this has been hinted at by Frontier as maybe what they were thinking, though as with many things (telepresence, artificial gravity, etc.) Frontier are probably better off
not pinning down a precise offiical explanation.
1) Engineered upgrades aren't all that difficult to build - after all, every faction is capable of fielding hundreds of engineered ships, every shipyard is capable of replacing your engineered ship. The reason you can't just buy them is licensing - factions aren't generally keen to allow this sort of technology to be in the hands of mercenaries as likely to use it against them as for them.
2) The Engineers are rare individuals (or heads of organisations) with enough shipyard facilities to replicate these upgrades, enough recklessness to be a "flag of convenience" licensor for them, and enough influence through some other mechanism (Palin's Thargoid expertise, for example, or Ryder's base being so heavily mined that no-one wants to attack it) that they're allowed to get away with this. And even they aren't foolish enough to license some of the really good stuff such as reverb cascade lasers.
3) The materials are primarily a payment for the
license, therefore, not the upgrade. The Datamined Wake Exception doesn't get printed out and put up inside the FSD to inspire the hamsters to run faster - instead, they're a payment to the Engineer. So obviously they charge more for the better licenses. And there's some highly anti-competitive cartel arrangements between them to ensure prices stay high.
4) All materials are, precisely because you can't buy them, in some way unique. That lump of Iron came from an outcrop on Bla Thua AC-B d1-17 6d. That Focus Crystal came from ship registration TY-198 and still has the scorch marks from its untimely demise. That Cracked Industrial Firmware is from a model RN380 Achilles robot illegally modified by its owner in 3184. They therefore, especially in large volumes, have considerable research value that a batch of Iron from the local mines or the factory-fresh focus crystals in the shipping container over there won't have. And the engineers are negotiating for exclusive access, so you can't just shop around that same CIF to everyone and you certainly can't pay the same engineer twice with it.
5) Recently this has, of course, generated a secondary market where people are willing to collect and trade documented-provenance items of interest to the engineers, and sell them (at highly profitable rates) to pilots. Similarly, the provenance requirements are somewhat at odds with the lifestyle of the average space pilot, so materials tend to be rapidly offloaded and transferred to a trusted custody authority - allowing things like remote licensing of the blueprints to take place in a secure payment environment, allowing factions to use documented materials as mission rewards without the actual object ever leaving some vault, all the conveniences of a modern economy.