No, the God of Catholicism is the God of all Creation. That means the entire universe, including time itself.
> Would non-human intelligent life have souls?
Catholic teaching is that all life has some manner of soul. Humans have rational souls. Intelligent life would therefore have souls.
> Why wasn't this mentioned in the Bible? Doesn't this mean that both creation stories are inconvertibly false?
Why would it? It doesn't claim to be comprehensive or complete.
> how could they square away the fact the vast majority of all life could exist without knowing salvation via Christ? Being ignorant of Christ doesn't automatically mean you are damned, but this now means belief in Christ is optional and kind of just a localized thing some humans choose to do
Many, many human begins lived and died without knowing Christ. Why would aliens present a problem? Perhaps they wouldn't even need it. CS Lewis wrote science fictions with un-Fallen aliens. Maybe such a thing could exist.
> if for example aliens claimed their savior was the "real" messiah, how could you dismiss that?
Catholics don't seem to have a problem dismissing other messiahs. Why would an alien messiah be different?
> events the Rapture essentially cease to make sense or will have to be radically re-imagined.
The Rapture as depicted in something like Left Behind is not how the event is generally understood in Catholicism or other sects. There's no reason it would have to change at all.