If they were trying to more faithfully reproduce the beer they found, they'd need to use all of the yeast cultures they recovered. (They commercial beer listed here was not actually attempting to reproduce the beer - just use the yeast)
There's some debate as to whether or not the yeast they're using is a contaminate, as well. Sacch strains do not seem to live long enough in fermented beer to make it 200+ years (though there's evidence that Brett strains will do just fine), and the samples were taken from bottles that had been decanted 20 years prior. The characteristics reported of the yeast are also similar to what many people find when using wild yeast. That might be due to them being wild yeast contaminates, or due to the selective "breeding" pressure of commercial yeasts having not yet eliminated these traits.
I wish they would sequence the yeast and release the results.
Except in this case, the starter is from a message in a bottle, lost at sea for 200 years.
Maybe something similar to it. Commercial breweries were selective in reusing batches of yeast even back then. House strains were refined over time to reuse batches that had fermented the most reliably, produced the fewest off flavors, etc. The yeast they used might also not have been local in origin.
But the wild ancestor might still be around, somewhere. (It's also possible the yeast they have is a wild yeast contaminate, as noted in one of my other comments in here)
There is also a hobbyist network of people that trade their local sourdough starter to people in distant lands, as dried-up blobs on index cards, through the mail. People also trade kefir, kombucha, yogurt, sauerkraut, kimchee, and vinegar starters. They wouldn't go to the trouble if it didn't make a difference.
The local ambient microbiome certainly contributes to the texture and flavor of fermented and aged foods, and it can be transplanted successfully for a few months, but then the locals usually overwhelm the foreigners. When you find a commercially significant one, you have to take great care to preserve it and keep it pure.
Yeasts do this with alcohol. Acetobacters do it with acetic acid. Lactobacilli with lactic acid. Other varieties exist, but their metabolites have less culinary importance.
But they probably didn't "survive" 200 years. In order to last that long, anything in the cold, dark, ethanol-contaminated bottles probably formed spores, going into deep biological stasis to await more clement environmental conditions. Not all microbes can do it, but the ones that can are considered very hardy. Yeasts tend to switch from asexual reproduction to sexual reproduction in nutrient-poor environments, and the resulting diploid cells can sporify.
The question is analogous to questioning whether a human embryo that had been frozen solid and stored in liquid nitrogen for 20 years is safe to thaw out and implant in a live uterus. It's just not a big deal for us. Sporing up and waiting a few centuries before thawing out the embryos is not a big deal for yeast.
Now that the pun's out of the way, normal discourse can commence...
 oh wait, all the comments are just other puns