I'm an undergraduate student of Molecular Biology and Genetics and I'll tell you my opinion, based on my current knowledge of how life works.
First of all, I might be wrong but I don't believe that our evolutionary ancestor and the ancestor of that bacterium had anything in common. Phosphorus is essential for life as we knew it and without Phosphorus you don't have DNA, no mRNA, nothing. You won't live for long if you don't have abundant Phosphorus in your system. Now, if that bacterium had traces of Phosphorus and a far greater amount of Arsenic, I'd be inclined to believe that it adapted, but something like that was not mentioned though. A radical change of Phosphorus to Arsenic though would be non-viable, in my opinion, because the bacterium would be unable to perform any essential life activity, even for a couple of minutes, which would lead it to death.EDIT: I apologize. I just now found and read the scientific paper and it mentions that there are traces of Phosphorus, minimally low as they are, but existent. At that level of Phosphorus, Phosphorus-dependent life would be unsustainable for the bacteria, but that might mean that it could be some sort of -radical whatsoever but perhaps valid- adaptation.
Now, alien or whatever? In my mind, I have two scenarios. First is that the first Arsenic-friendly cell appeared along with the first cell who used Phosphorus, but was surpassed by the Phosphorus ones, just because the latter were able to adapt much better to a wider range of environments. So, today we only see remnants of life with Arsenic, since this planet was hostile to it, for lack of Arsenic.
Another -perhaps less possible- scenario would be that these bacteria were transmitted to Earth on a meteorite or something. You know, back when dinosaurs roamed the Earth, there was an era when Earth received hundreds and hundreds of meteorite hits from outer space. Perhaps, some meteorites with bacteria on them hit the earth at various sites. Those who landed on an Arsenic rich environment managed to live, while the others perished.
Just some of my thoughts and please do not take any of them as scientific truth. I'm only an undergraduate student of Molecular Biology and Genetics, who aspires to be an Evolutionary Geneticist one day.