I imagine that even with fabricators, we're still going to have specialized manufacturing...areas? Zones? ...not to sure on what exact terminology to use, but the point I'm trying to make is that we'll likely still have regular factories and manufacturing complexes dedicated to specific industries and products, rather than just replacing them all with 'general' fabricators.
After all, having a system dedicated to making, as an example, isolinear chips means that we'll be having a steady stream of those constantly being made, so if we ever need more, then we could just dedicate a bit of fabricator power to assisting them or simply build more factories as opposed to needing to constantly be micromanaging what we're using the fabricators for like we likely would if we just replaced all the factories with general fabricators. The various equipment pieces will likely be upgraded and/or replaced, perhaps with specialized fabricators that'll be useful for a specific industry's needs, but I think that most industries will remain active.
If I had a guess? I think we're basically going to end up with something that... Well, I believe there's three Quest Systems that do a good representation of things here. The first is this Quest, with it's Indicators representing both an inflow/outflow rate along with 'in reserve' quantities. The second is another quest on SV called For The Tyrants Fear Your Might and there it's basically a 'thing' where the question isn't '
do you have this in production and what are your production capabilities?', it's purely 'So this is how much of a given resource type we have, how long and what can we produce with it factoring in our already existing resource income and expenditures?' with any lack of industry meant with the answer of 'so use the fabricators in your garage to build up more of the right type of fabricator to build the actually needed fabricators as fast as possible!'
The third one is the one I think is going to be the case for GDI going into the Sequel and that is the Saga Of Legends/Space Mecha ___ Quest Setting group of Quests over on Space Battles. As they basically represent a 'halfway point' between the two mentioned above. That system divides resources into Minerals, Rare Minerals, Organics, Light Industry and Heavy Industry, then making mention of when certain specific things are plentiful or running short. Over there the big ones tend to be 'actually quality food, especially the various luxuries', 'FTL Drives', 'Antimatter' and 'Fusion Fuels' with that last one basically representing the fact that the local area is extremely underdeveloped so the lack of fusion fuel is just no one has gotten around to building the fuel extractors... Or the local war/conflicts happening have gone around blowing up said fuel extractors.
In that system, Minerals, Rare Minerals and Organics represent the 'raw materials and basic upkeep goods'. Minerals being more or less 'any industrial material not grown or usually identified as organic-related' (I'm not sure where complex hydrocarbons fit, but I suspect it's probably Organics). Rare Minerals is 'stuff that is hard to get in bulk, exotic resources or low-level processed goods you can't easily mass produce'. More or less 'yeah, you can get a bunch of this but you probably aren't measuring it in kilotons of output despite the fact it's invaluable for good quality or complex anything'. Our STUs would most likely fall under 'Rare Minerals' for example. And Organics is the various foodstuffs, things you get from processing growing organisms or other related-to-organic-lifeforms substances, so micronutrients, medicines and more would all fall under this just as much as cotton, wood, algae-based rations, complex hydrocarbons extracted from bioreactors and plastics would.
But the important element are those 'Light Industry' and 'Heavy Industry' categories. Because those more or less represent 'Fabricators, and other Light Industrial outputs which can be produced by fabricators but might benefit from having dedicated factories produced for them'. An example being that a single 'point' of Light Industry means a given colony has more overall industrial output and also might, for example, decide to set up a dedicated Mech-Farm meaning that their production of Mechs is higher quality, more reliable and efficient, faster and doesn't require that they constantly divert the fabricators to producing more Mech Components instead of other industrial goods needed by the colony.
Heavy Industry meanwhile? That's stuff where fabricators just can't manage effectively or at all. So if you want to produce advanced electronics? That's Heavy Industry. If you want to mass produce ships in squadrons rather than doing sort-of-bespoke builds slowly? That's building a 'point' of Heavy Industry and specialising it in Shipyards. Sure, the existence of Heavy Industry at all massively amplifies your colony's industrial capabilities but unlike Light Industry, it is very focused on getting one type of Industry done
well.
TL
R the unlocking of the two levels of Fabricator tech basically means that all of a sudden all the minor projects from Light Industry, Agriculture (to a limited degree), Heavy Industry and more get piled together into generic 'expand industrial capability' projects because we've got
some capacity in that demand just from diverting the fabricators over to producing that good. With an expansion of industry meaning that we can keep a handful of fabricators dedicated to a single task and all around need to change around what the fabricators are producing less often.
Whilst the Major Capstone Projects becoming shorter due to greater ease producing the supporting elements yet still stick around as they represent building up focused effort for a single, complex type of industrial output which the fabricator complexes either can't produce (looking at Isolinear chips here for example) or can only produce lower quality, reliability or technical capability versions. An example of that last one being that Fabricators most likely mean colonies are able to produce their own microelectronics, but they can't produce the 'modern', let alone top-of-the-line, microelectronics until they set up their microelectronics industry. But hey, if the colony got completely cut off from the rest of galactic society, they'd only fall back to the early 21st century technology capability so long as they make sure to set up the needed industry to maintain fabricator availability.
This is all my viewpoint of course and I can absolutely be wrong or misunderstanding something.