The original creators probably didn't put much thought into it but, how did the logos come about for the Transformers? How did the Autobots come up with their logo? And the Decepticons? When I thought of this question, the first thing I could think of for the Decepticons was that the insignia is the representation of the Alpha-Decepticon, the perfect one. A symbol of perfection in power. But then again, Megatron is the founder of the Decepticons. Surely if he would recognize himself as the perfect one. Any other ideas?
Toys - the faces were based on Soundwave and Prowl, I think it was. Fiction - it varies. In IDW's Megatron Origin, the Decepticon sigil predates Megatron, being associated before that with the gladiatorial combat arenas that gave rise to the Decepticons. Megatron merely took it as the symbol of his uprising, as he put it "the badge never comes off" Marvel's G1 has one of the first creations of Primus, the Last Autobot, with a very Autobot sigil looking face. Since that particular robot was a legend even among the Decepticons, you can imagine the face was passed down among those who followed the Last Autobot's path. I think the cartoon might have explained the sigils as being something to do with the Quintesson's branding - military exports have the purple one, domestic products have the red one.
I can't remember where i read this, but Vector Primes face looking like the autobot symbol might have something to do with it too (as he was one of the 13).