Reciprocally-linked trillum and CG autofacs will output way more of either resource type than if they are unlinked, which is a core game concept. Since trillum and CG are so vital, almost every planet in an advanced empire will be in some way reliant on functioning trillum-CG autofac pairs or complexes, sometimes linked through hubs.
The way that trade routes work right now is that priority for importing resources in shortage conditions seems to depend on the order in which trade routes were established. In situations where there is more demand than supply for trillum and no stockpile, you can get situations where other planets claim first dibs on the trillum planet's output while CG autofac planet(s) gets shorted. This ultimately results a joint economic collapse because the CG autofac is no longer fully supplying the trillum extractor, which must bring its own CG autofac structure online to make up the difference, resulting in even lower trillum output, so the CG autofac and other planets get even less trillum, etc.
The same is true in reverse, where trillum extractor planets get shafted because CG autofacs are giving all their output to other planet designations and nothing is saved for the trillum planet.
Trillum and CG shortages are the only shortages that directly kill planetary populations and cause social order penalties severe enough to incite civil war. (Survival goods too, but these use trillum and are manufactured locally). Trillum and CG autofac planets should always get top priority for receiving CGs and trillum respectively, ahead of other planet designations.
Foundations and sector capitals should probably get dibs after Tr and CG planets but before other planets because civil wars on sector capitals are more dangerous than civil wars on other planet types, and because foundation-supplied-TL shortages can also cause economic cascades.
Yards should get dibs on all mineral resources ahead of autofacs and mineral extractors, tying in to http://ministry.kronosaur.com/record.hexm?id=59679. It's not uncommon to see ramjet yards underbuild because chtholon processor worlds are consuming all the aetherium, even though chtholon is useless on its own since all ramjets require aetherium too.
Hubs already try to meet their own full demand before they apportion resources to other planets, which is fine albeit somewhat wasteful since the hub itself can't do anything useful with its labor pool other than build planetary defenses.
There is also inequitable resource pulling in non-shortage situations in some cases. This is mostly an issue with planets that build individually high-cost units like starcruisers and exotroops.
For example, a low-population starship yard that builds 1 or fewer starcruisers per cycle always requires 1 or fewer reactors per turn. If it is being supplied by trade routes from two autofacs, it will always try to pull the reactor from the route that was established first and will never pull from the second trade route at all. This makes it difficult to ensure that low-volume planets get properly supplied by direct routes, unless you connect several to the same hub (so that aggregate demand is high enough to be divided across multiple planets.)