Wait. What? So you're asking "If the Terminator universe and the Fallout universe found themselves occupying the same space/time coordinates, and each of them broke their own way of being (i.e. terminators siding with their humans on one side, and the BOS and Enclave joining forces on the other), which universe would win?"
1 - The Terminators would not side with the humans. They are at war with humans, and it seems doubtful to me that they would side with one group of humans to fight another group of humans. Also, do you really think that the humans from the Terminator universe are going to suddenly side with the Terminators? It seems much more likely that they would notice the new (Fallout) humans and try to side with them instead.
2 - Although it is more likely that the BOS and Enclave would form an alliance than the Terminators/Humans, I still don't see it happening. However, both the Enclave and BOS would probably be having multiple orgisms if they could sieze terminator technology and be able to use it.
3 - The Terminators have a huge advantage over all the other parties involved in that they have and use time travel technology. Although the humans from the Terminator have managed to get some limited use from terminator technology they've acquired, they still don't have the means to make it themselves.
Due to the time travel technology alone, I think the Terminators would eventually be the victors.