I saw a comment elsewhere along the same lines. My take on it is twofold:
First, the only things you can make in a factory that are strictly equivalent to standalone buildings are power generation, fuel generation, storage space, conversion capsules, and monetization stations. That’s only about half the things you can build, as monuments, mines, the pollution resistance of residences, smokestacks, energy relays, turrets, and command centers have no in-factory equivalent. Yes, factories can house citizens, but they don’t protect them from pollution, which might not even matter right now but I think is worth noting. Finally, devices that generate waste take significantly more time for your employees to manage than their standalone buildings do.
The second is the roadmap, and the conveyor hidden away at the bottom of the build menu. One of the eventual features is transportation and trucking. Seems to me that the current environment of ‘fuel automagically transports itself into your generators’ will go away eventually, to be replaced by a logistics management in the factory building screen, which will likely wind up making factories less powerful by comparison to the standalones.
So, yeah, factories are better at the things they do than the standalone buildings would be, but I also wouldn’t expect that to last as more features come out.