I think this is a frustration a lot of players have brung up previously, that factories have no real purpose. While personally I'd also like some form of game mechanic associated with them (eg, a use for the parts besides just making more things and selling them), it's a purposeful design decision to have them be crafting only.
Imo, it's intended so that there is more endgame content that is not actually required. You can easily continue playing without working on factories for as long as you'd like. That's not exactly the case with power creeps or boosts or things like that. There is an opportunity cost to ignoring factories, they represent a significant economic potential. But you don't actually have to work on them if it doesn't appeal to you.
In that way, I think it's a good choice. If you like crafting and logistics challenges, you can work on it. But it's not like you'll have a significant gameplay disadvantage (towers are half as effective or something similar) if you don't work on it. @o4kapuk can provide more details.
Two things of note: Factories will effectively increase the size of the market, since you can sell things much further distances when compressed. Prices will likely be affected by that. And for the record I personally find the idea of creating gameplay things with factories like bombs or special buildings cool, but I respect and understand the design choice involved.