Prime was a term of art in the discussion of alternate universes which designated whatever the speaker regarded as the "main" universe, timeline or even Earth. Thus, phrases like prime universe and Earth Prime were common to those who talked about such things. A version of Melanie Bush once thought that everyone across the many parallel universes would assume that their Earth was the "prime" one. Indeed, at least one version of the TARDIS could be programmed to travel to an "Earth Prime", which was presumably in the same universe as the "Gallifrey Prime" of that TARDIS' origin. (PROSE: Spiral Scratch)
The Eighth Doctor was witness to numerous prime realities shown by Zagreus. (AUDIO: Zagreus)
When Zagreus showed the Eighth Doctor of the positive-time universe the billion alternatives of anti-time, the Doctor wondered which reality was the real one. Zagreus stated that they were all real and primary to their inhabitants, usually existing separately but sometimes sharing eras. These other prime realities included one where the Eighth Doctor visited Oblivion, one where the Eighth Doctor removed his own heart, one where Gallifrey was replaced with a timeless diamond, one where the Time Lords had "terrible mind powers", one where the Time Lords were removed from time, and one where Nestenes nearly destroyed the Earth. (AUDIO: Zagreus)
They are all real, and primary to their inhabitants. In the grand scheme of things it doesn't matter. Who is there to care? They all exist, occasionally sharing moments and eras, the rest of the time self contained and unaware.
Lethbridge-Stewart's universe was considered by the Accord to be the primary reality from which the multiverse branched. (PROSE: Home Fires Burn)