With the speed of light being as slow as it is, that Alien must be very long lived to consider such a trip. The PhD should start observing the dinosaurs and for lack of enough data continue on to humans.
The presumption that "today we know precisely how the universe works, and therefore, all stories must follow this mindset", is odd here.
Would you insist that Newtonian physics was the Only Way to Think of Things, prior to Einsteinian? Why, then, do you presume this will remain static forever? And therefore, suggest that a story should follow this logic?
While it is possible relativity is wrong, anything that replaces it must fit all the observations we have about the universe that we currently use to prove relativity. That leaves very little room for the replacement for relativity to be different.
Newtonian physics is a special case of relativity when you keep relative speeds slow.
We don't know how quantum mechanics fits in. There is a known hole in current physics. However the size of the hole is small.
I find it difficult to respond without emotion, to such a comment. We likely know very very little about physics right now.
My point with Newtonian physics is that at the time, it was The Physics. According to observation capable at the time, it seemed to make sense, with a few little oddities.
To them, they thought they had a small hole in current physics. Does that sound like your "small hole" in current physics today?
You believe we are knowledgeable, for we posses knowledge our ancestors do not. You believe we are right, for our observations tell us so. Yet how will we observe the universe 1000 years from now? 100? What tools will we have?
Place yourself 1000 years hence. Our ancestors will look back, and see our current physics as we view Romans babbling on about The Elements and aethers. Yes, to our descendants, our science is absurdly simple, filled with holes, broken, the list goes on.
We are not even remotely sure if space/time is consistent outside of our local region of space!
Back to your Newtonian statement, what if all of our current physics was thus? A viewpoint which only worked under certain circumstances. From where I sit, this is the reality.
We work with what we have, but must keep the knowledge of our massive ignorance in play too!
The reality is newtonian physics is still taught in college because for the vast majority of what people need physics for it is close enough to correct as to not matter.
I come back to this: even if we are wrong, whatever is correct still needs to fit all the observations that we have done to date. I don't know what we will know in 1000 years. Euclidean geometry is over 2000 years old and still considered correct (though we have expanded on it a lot - see in particular non-euclidean geometry)
That fact that we are ignorant doesn't imply FTL is possible- that's optimism on your part. The universe doesn't care about your optimism and has no obligation to contain the physics that can make Star Trek a real thing.