I have noticed that when I get the second ideology in the Motivation line for Malevolent (Relentless) it seems to apply the +10 manufacturing bonus to both my homeworld and the first world I founded.  "Relentless +10" clearly appears on the manufacturing tooltip for both planets and the number reflects this.

Additionally, when I get the third ideology in that line (Ruthless) the 100% military production boost is also applied to both the homeworld and first colony.  Even with 100% science allocation, they have "Relentless +10" in manufacturing and the military production is 20 (assuming a full military slider).

Is this intended to affect more than 1 planet?  For reference, this has happened in every game I have played with malevolent (which is only 2) and the first colony is never in the same star as the homeworld.