Scenario 2 is not good for the Flood. Star Trek is just full of weird species and creatures that wouldn't be susceptible to the Flood. See: The Crystalline Entity, the Giant Space Amoeba, various space cloud organisms, Armos, 'God', V-Ger, Silver Blood, Medusans, Horta, Wesley's Nanite species, and almost certainly things who were already cellularly mutable,
used high-end-nanotech, or both like the Changelings, the Borg, and Species 8472. Worse, the Borg at the very least have their
own time travel capacity, and would quite happily use it to ensure that any assimilation happened under their own terms.