Took part in an online rpg a long while ago where the we weren't really to know about the villain's motives. Turned out we were in a time loop created by him, where he was trying to prevent the split of a timeline into multiple realities, but failing over and over again, in escalatingly violent and drastic ways. We finally broke from the loop, but the villain went back for another go in order to escape. He wasn't evil exactly, just believed that what he was doing was absolutely necessary, and was getting more desperate all the time.
Turns out that timelines splitting off from each other was a natural occurrence in that game, and preventing it could have caused all realities to collapse in on themselves.
As for Unicron, I never saw him as originating as a multiverse being. More like the Borg, where different Unicrons across the multiverse just decided to network into a hive mind after they found each other. That still means he could be trying to merge the multiverse into a single reality (and is somewhat successful, as seen in the Universe setting) instead of merely being a nihilistic anarchist glutton. His motive could range anywhere from ruling all as a hive mind, to making ginormous softball team out of the other Unicrons. I still think he hates Cybertron/Primus though, for whatever reason.
As for BW being in the original reality, we can look at Gaia as a reference point: devoid of Humans in the future of BW2/BW Neo. It is possible that the actions of the Axalon, the Vok, and the Darksyde crews (and specifically Waspinator) eventually lead to the demise of Humans on Earth, causing a paradox where the Golden Disk was never created or launched, meaning Megatron (Decepticon) never wrote the message and Megatron (Predacon) never stole it or headed to ancient Earth in the first place.
The results probably would have shredded reality, desperately trying to fix itself right from the start so that at some point there would be Human beings to create and launch the Golden Disk. A multiverse would minimize the effects of a paradox.
Edit:
If that's all somewhat true, it means that the Golden Disk is the single most important artifact in Transformers history, even above the Autobot Matrix of Leadership. Glad I got mine from Unicron.com
