Well this is how I would add the tranformers to it
The Autobots would act like how angels usually are. Protectors, mentors, teachers, that sort of thing.
But the Decepticons are demons. Megatron is completely aware of the SEEL/instramentality conspiracy and so decides to just bide his time and only send the other Decepticons out to keep the autobots occupied/stop them from suspecting anything. But what's interesting is that who he sends out is intended to mock the conspiracy in some way.
the belief that being a piolet makes you special and the dummy pug - Vehicons and their disposable nature
Tokyo 3, a testament to engineering - Constructicons can build some thing better and tear it down
The idea that you shouldn't form attachments because they will just leave you - Airachnid, "Got any partners I can STEAL"
The 3 piolets working in harmony and how the MAGI works - TFA Blitswing, 3 faces of madness.
Misato the strategist and Kaji the spy - Soundwave, the child they could have had that would show them both up.
Rits buying the idea that humans are at an evolutionary dead end - Shockwave, the tp insecticons, and tp predicons "Evolution does not work that way."
The dynamic between Gendo and SEEL- StarScream
Gendo a petty delinquent - Steel jaw one of cybertron's most wanted
"By becoming one in body and soul we will achieve peace" - Menasor
Megatron himself is also not above showing off something wrong with the conspiracy. SEEL, "Humans are fools only capable of harming others." Megatron would say that if that was true humans would last longer than five seconds in the pits of Kaon.