There aren't multiple versions of Primus. There is one Primus, but he exists in all realities at the same time. Gods can do that you know.
Anyway, I went back through the Ultimate Guide to do some research and copied down a load of information about Primus and Unicron's origins, proboably more than would be wise to try and post verbatum, though I can if you want me too,
, so I mwill summerize it as best I can.
In a nut-shell it states that Cybertron and the Transformers exsisted even before organic life crawled out of the primordial ooze on Earth, and that Cybertron is really Primus, a being forged when the Universe was still in its infancy. It goes on to say that Primus and Unicron were created by The One at the dawn of time, originally as one being, then split into two, one Unicron, the other Primus, to explore the Universe and all of its realities, spreadin ghteir entiretiy accrossnew planets and realities, creating new worlds in them all and thus seeding the future, but Unicron descended into destrcutive rage and began to consime and destroy all they had built forcing Primus to take up arms against him. It states that both Primus and Unicron took on an astral and physical planetary forms with robot modes, though Primus rarely uses his and passed his ability to transform down to his creations, preferring instead to be a part of the Universe and all of its realities on a planetary level, feeling its ebbs and flows. Primus created planetary turbines within himself and created a crew of 13 sentient beings to guid and maintain his planetary form, but one betrayed them, joining Unicron, and most were destroyed in battle with him, though he and the Fallen were cast into a black hole. Afterwords, Primus established an orbit around Alpha Centari. (pages 10 and 53)
Under the page on Unicron, it states specifically that he is committed to the destruction of all life and has crushed and consumed planets and infected the very substance of space with a chaotic virus that undid the very Order of the Universe, then when nothing remained, he would rest only to awaken again to move on to a different reality to start the process over again. (Page 50)
Further, and this I will qoute directly, it states,
Unicron would return again and again, and could be temporarily defeated but never totally destroyed. Each time Unicron replenished itself, its evil grew and it adapted its body into new and different configurations. Its vast heavily shielded Spark Core was resistant even to Matrix energy allowing it to rebuild by absorbing other sparks or pure Energon.
(page 51)
The Ultimate Guide also goes into the
Armada comics, where Unicron had pulled heralds from one alternate "G1" reality, including a "G1" Galvatron, Scourge, and Cylonus, among others. Once again showing his ability to transverse from one reality to another. Primus' physical form, though, never leaves a given reality, yet, he exists in all of them as the same being because there is only the two of them: One Primus, and one Unicron, born at the dawn of time itself.
As fro the origin of Primus being capable of existing in multiple realities at once while still remaining one being, and Unicron travelling between realities, I believe the 3H and Hasbro
Universe story lines initially established that retcon. They even retconned the Quintessan origin of the cartoon in
Wreckers #3. This was further confirmed in the Ultimate Guide and the DW comics where much of the information for the Ultimate guide is from.
Again thanks for the compliment! 
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