Sure. A dumb civilization could have done it too, perhaps as something to do with crystals or the Zodiac.
But in all seriousness, Occam's Razor is a great tool here. So far, every cosmological problem we believe we've figured out has occurred due to natural processes. There is very likely something we don't know about large scale structures (an understatement!).
* All intelligent life goes extinct before achieving interstellar colonization, or is content to remain in their home stellar system.
* We are in the first generation of life in the galaxy capable of achieving interstellar colonization, due to the time scales required for sufficient heavy elements and evolutionary complexity to arrive.
You’re not downvoted because you suggested the existence of aliens in general. Sure, we all hope that there is intelligent life somewhere else in the Universe or even in our own galaxy. But that doesn’t mean that every cosmological mystery we find we’ll attribute it to some advanced civilization.
Besides, even if this was the works of some super duper advanced civilization what difference does it make? Our quest is to explore and learn new things, whether they were made by nature, God, or any freaking alien out there is irrelevant.
SETI exists for that tiny, tiny chance that in the few years (very, very, very few) we look at data, the Earth is receiving transmissions from a remote part of the universe. Voyager's messages are far more likely to make contact with an alien species, since they'll be around effectively forever. It's just a matter of whether that happens while we're still in existence.
Voyager's won't reach the nearest star before 40,000 years, but, dunno, are any of the two actually aimed at any neighbouring star?
I mean, come one, having a Voyager pass by some anonymous star at 170 light years of distance in 1,2 million years, and never come closer than 2650 AU to the star, what's the chance of actually detecting it by ET - even if an advanced civilisation is (will be) watching from one of its planets. It's tiny and, by the time it arrives, even the radioactivity levels will have dwindled to nothing. The only things that would make it stand out is it's speed, and the fact it's made of metal. They would need a very advanced radar, capable of detecting tiny masses of metal at enormous distances. Then, to investigate it, they would basically have to go grab it - but would you justify hunting for any chuck of metal transiting by the Oort cloud - what if it were just a piece of debris from an asteroid?!
But you don't know what advances would happen in 40,000 years, that too on another solar system. Maybe alien kids would be playing in their back-yard beside their Oort cloud equivalent and might check out Voyager just for fun.
Seems far more likely that in 40k years, humans will have discovered the ability of interstellar travel. Heck, at that point we could go out and fetch Voyager 1 ourselves before it comes within 1.6 light years of AC+79 3888. If we can't in 40k years, it's likely not possible that we'll ever leave this solar system. It could be that's it's just not physically possible. But more likely, do we survive long enough to develop that technology?
I've always viewed the Golden Record as a way to make humanity feel better about its future. The need to leave a legacy behind is core to who we are, and that's exactly what we did with those two discs. We left something behind that will survive for 1 billion years, with the infinitesimally small hopes that someone will find it. But, it makes us feel good.