Interesting.
Be aware by the time of the Beast Wars, Unicron has been physically destroyed -- presumably since G1. He only exists in spiritual form known as Dark Essence or Angolmois Energy. When Unicron destroys the Maximal Armada, he is still in spirit form, albeit fully powered by his Angolmois Energy (and using BW Galvatron as a vessel) -- then he possesses Vector Sigma and begins reconstructing Cybertron as his new body. All this would be needless if he already had a reconstructed body as you've suggested. So I don't know if you really want to keep the story of him having a new body, otherwise you'll need to find a way to have that body destroyed. But one would assume that if the BW TFs had recently destroyed Unicron, they would be more aware about the nature of Dark Essence and Angolmois Energy than they already were...
Also, other agents of Unicron include the Blentrons, Shokoract, Antagony and Cataclysm.
Also, Tripredacus was never made from Cybertronians. Neither was Tarantulas. That's why Tarantulas was willing to destroy the Ark and kill all the Autobots and Decepticons inside them, wiping out the existence of Maximals and Predacons. When asked about this supposedly suicidal plan, Tarantulas boasted that it would only effect Transformers "descendant from Autobots and Decepticons" and that he and the Tripredacus Council have "different origins" (and thus were immune to being uncreated at the destruction of the Ark).