Yeah, virtually every cybertronian in this universe acknowledges the existence of Primus, Unicron, the Thirteen, and everything else that happened in The Covenant of Primus. The differences in faith mostly come from how much individuals allow it to affect their daily lives, and how they go about practicing. You have folks like the Knights of Cybertron and the Angelicons, who devote themselves to specific organizations and their practices, and then there are guys for whom faith just isn't very important, along with everything else in between.
There's the different crests that each of the Thirteen had, but that's pretty much it for icons. Gestures, prayers, and the like depend upon whatever organization you're a part of, if any. Some have specific rituals they perform regularly, while other bots are content to just say a quick word to the Bot Upstairs whenever the mood strikes them.