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There is a recycling system expansion bay for starships that states:
Note: The following Expansion Bay is compatible only with a Supercolossal ship.
A recycling system enables a Supercolossal starship to be nearly self-sustaining, operating independently for decades or even centuries. A combination of smelters, biomass processors, manufacturing, and UPB converters allows the ship to convert almost all its waste into goods and materials.
It appears that items can be broken down into UPBs with "smelters, biomass processors, and manufacturing." I assume the "UPB converters" then convert the UPBs back into useful items.
The recycling system is the size of a cargo bay, and it can convert "almost all" the waste generated on a starship into UPBs.
So, the raw materials for UPBs seem to be almost everything you can imagine. As to who makes them? Probably any organization with the resources and desire to make them.
Technological devices don't appear to be the only way to make UPBs. The stat block for the Assembly Ooze states the following:
Thought to have been created on the planet Bretheda as a biotechnological replacement for automation processes, assembly oozes are essentially cores of nanobots suspended within blobs of animated protoplasm. As the ooze absorbs raw materials, the nanobots work at the molecular level to turn that matter into a functioning technological device, the blueprints of which have been entered into the machines’ original programming.
The Assembly Ooze can only make "virtual UPBs," but it does appear that UPBs might be created by both biotechnological and normal automation processes.