They released a comic from the TF Collectors' Club called "Another Light." Near the climax, Nexus Prime, one of the 13 Original Primes, uses the Star Saber and the Terminus Blade to strengthen the barrier between universes, much to the disagreement of his fellow 13 members. As a result of this, Primus, Unicron, and the 13 are no longer interdimensional beings, and separate versions of them can exist in every universe. This allows for future stories to tell the story of Primus, Unicron, and the 13 in any way, and for membership of the 13 to freely differ from universe to universe.
As a result of this, Primus and Unicron have changed personalities in the SG universe. SG Primus now regards his inhabitants as an infestation (not unlike TFP Unicron), and SG Unicron is now noble and tries to help the good guys out.
To be honest, I'm not entirely sure that I'm on board with this change. On the one hand, it does admittedly allow more room for creativity, and I'm all for putting new and interesting spins on things. However, on the other hand, it kind of gets rid of consistency, and I rather liked the idea of Primus, Unicron, and the 13 being these constant islands in a multidimensional sea of variation.