Synthetic buildings (aka factories and research buildings) are twice as strong as the organic variants. 5% vs 2.5% for basic on up (almost, top buildings are 20% vs 12.5%). Back this up with no need for approval/morale buildings, farms (even if it is global), or cities and you can fill a planet with nothing but factories/research, plus synthetics still get a centerpiece building for adjacency bonus builds. The only weakness I see with them is economics for credits though a well built factory planet can build out strip mine projects at a rate of one per turn for 25 credits.
I would like to see an official response to this topic from Stardock but my analysis of the XML data files (and the various changes from 2.0 to 2.1 and subsequent patches) makes me wonder if your assumption about the differences between manufacturing and research buildings between Synthetic and "standard" race buildings being truly intentional. But I would be happy to find out that there was actual thought behind where we are now !!!!
While you don't need Power Matrix buildings for Population growth any more with the change to Synthetic Races getting a global change to PopulationCapYor to 100 and Morale (GoodsAndServices) to +100 in the Ability.XML file changed in the 2.14 Opt-in Patch, these buildings did provide for adjacently bonuses when used with the other Manufacturing, Research, and Economy buildings just like Ancients (Altarian) get with the Social Matrix buildings, Paranoid Races (Iconians) getting with Molecular Fabricators, Slavers (Drengin) getting with Slave Pits, and Thalians (whether you consider this a Knowledgeable or TimeTraveler Ability) getting with Hives (if they ever return - Draginol had mentioned they might in the "next" patch).
The Spark of Life Techs and Assembly projects allowed Synthetics to gain "growth" benefits that other races get with their Population Growth buildings. Especially since population now is the main effect to the Raw Production for a planet.