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As of this writing, neither Unicron nor Primus has appeared in the new IDW comics universe. Writer Simon Furman has outright said that this universe will have "no Primus. No Unicron", while hinting IDW may be "poking and prodding around the pre-history of the Transformers... the very beginning".  IDW publisher Chris Ryall has also stated "we're also going to do the TF origins this year , too. That one will be called The Thirteen". 
While author intent on its own could still leave room for an IDW Primus, if the upcoming story has a contradictory origin for the Transformers, that would retcon out the previous retcon, rendering Primus as being once again a feature of only some Transformer continuities. (And then some poor sod would have to heavily edit this article.)
It is confirmed that there was a Primus in some shape or form, as Cybertronians were shown taking his name in vain while under attack in Megatron Origin, part 4. Furman's explanation for this in his blog is that this is not the G1 Primus, but it is possible there was "something or someone" called Primus at some point. 
In the absence of Primus, there were some other interesting things to mention in Cybertronian religion. In the Stormbringer miniseries, Jetfire and Scoop make mention of Primacron in an almost religious manner ("Primacron help us" and "Primacron only knows"). Bludgeon claims that there is a spirit of Cybertron which needs to be appeased to restore Cybertron, which one could easily interpret as Primus. However, Bludgeon's idea of appeasing Cybertron was to allow Thunderwing to destroy a bunch of planets in a mass sacrifice, so his sources (and his sanity) are a matter of debate.