Sure, there are a lot of reasons one can imagine that make that untrue, but the point isn't that it is impossible, but rather that there are other explanations that are significantly more likely even though they themselves are unlikely.
We have 0 examples and 0 evidence of advanced alien intelligence. We have rock solid proof of human intelligence on earth, and several examples of magical-seeming technology in the hands of some of its people and not others.
And again, this argument is predicated on the rather debatable assumption that the phenomena in question is indeed a craft of some kind. We have a ludicrous number of examples of human beings ascribing natural phenomena to magic and/or aliens.
As you suggested, it is unlikely that a futurist from a newborn civilization would accurately predict what a million (or billion) years old advanced civilization would actually do, and I am also legitimately unaware of whether we have any reason to believe that such projects would be visible when we can barely make out the closest planets outside our solar system (and only indirectly via math). Or if someone blotted out an entire star, how would we know? We use a term called dark matter to fill in the 75% of the universe that we can't describe in conventional terms. As some people posit on this subject, do animals in a nature preserve know they are in a nature preserve? Doesn't look much different than their world did thousands of years ago aside from occasional ufo's flying overhead (planes) unless they stray toward the edges/out of the solar system.
Btw, I would have been one of the skeptics writing these comments three years ago pre-Nimitz release (in fact, if you go back far enough in my HN history I found some comments saying that if there was a greater intelligence it would just ignore us LOL https://news.ycombinator.com/threads?id=lend000&next=1418634...). If you study this incident and a whole plethora of other phenomena with an open mind, you'll find some pretty damn fascinating things from various places with different agendas and levels of credibility (it is certainly not 0 evidence) with significant implications.
It is evidence of something going on that we do not understand. That does not immediately mean aliens any more than it immediately means magic or god.
Skepticism is important to keep discussion grounded, and I appreciate the level headed discussion. To me, finding something that breaks our understanding of reality is just as interesting and worth pursuing aggressively regardless of which of the above explanations is most correct.
When you consider the, quite literally, astronomical distances involved in interstellar travel and the corresponding time and resources required, combined with having no data whatsoever to suggest that advanced intelligent life exists anywhere within our galactic neighborhood, aliens look like a pretty damned unlikely explanation.
Hell, it's more likely there's some Wakanda-like hidden advanced human civilization somewhere around here, or maybe a non-human one that inhabits our deep oceans or something. Even less likely than that is some form of time travel from future humans which, again, is still more likely than aliens because we know with certainty that human beings exist on Earth.