I think it's the intention. Blood is what powers the organs, right? Energon, blood of Primus, will power those "organs" who belong to him. In theory it should be all Cybertronians but since Decepticond don't share the ideas of the God of Light..... hmmm.... they still seem to need it. Perhaps they are not all doomed traitors of Primus.
Whatever, it seems those who serve Primus are powered by his Energon while those who belong to Unicron would be powered by dark energon. The deceased obviously fall into the later category, but it's not only them.

Raf obviously belongs to Primus since he reacted well for the energon.

 

I dunno.

Whilst I think a demented bot how eats everything in sight can work for Unicron.
And prophesies can keep Primus alive in a sense.

I'm not sure if this Prime saga will go down the Transformer 'GODs' road.
I could be wrong.
But TFPrime like the movies seems to want to keep this saga semi-realistic.

 

"It dominates and destroys everything it touches" according to WFC Starscream. Megatron immediately dominates Dark Energon. I know it isn't exactly in continuity anymore, but I imagine it makes Arcee weak because she isn't dominating enough to control it.

 

Arcee is strong enough to fight it.

 

That's a pretty good explanation. Makes sense to me, anyway.

 

I wonder if Dark Energon also turns a living Cybertronian into a undead one, and whether the exposed or infected individuals retain their consciousness or will depends on their personalities.