I am not sure what the pre cook adds to flavour or texture? Is it really worth the risk? Even if it's very low?
The pre-cook does all the things that dry-aging does (besides concentrating flavors by desiccating the meat). But because of the higher temperature it works many orders of magnitude faster. It increases the tenderization by the same methods as aging, and it increases the level of dry-age kinds of flavors.
And of course, it's completely optional. You'll get great results without it. I just don't think the risks are significant, if you're careful about pasteurizing the meat's surface first. I summarized the bacteriology in the article. Basically, at 40°C, eColi populations double every 30 minutes. Which means that over the course of four hours they'll multiply by 256 times. So if you start with a pasteurized surface, which means the original number of pathogens on the surface have been reduced by 6.5D (10 to the minus 6.5 power, or 0.0000003), the pathogen population is still less than 1/10,000 was it was when the meat went into the bag. This is overkill (literally) by many orders of magnitude.
The dangers, however slight, aren't from pathogens directly, because any bacteria or virus will be killed by the cooking once you turn up the temperature. These long cooks always pasteurize the meat all the way through. Some bacteria, if the colonies become active enough, release heat-tolerant toxins that can make people very sick. I have never heard of this happening with a long sous-vide cook. The other issue is spoilage bacteria, which I address briefly in the blog. I have indeed heard of this problem showing up in the sous-vide bag, but always without a pre-pasteurization, and usually with some other funny business, like a long cook of meat that's been rolled (so there's contaminated surface on the inside, where it will take a long time to come to cooking temperature). The results of spoilage bacteria are disgusting but not life threatening.
Questions I'm more interested in are how big a difference does the pre-cook make? And is there a more optimum time or temperature? I'd like to do these experiments, or convince someone else to do them. All i can say now is that science supports the general idea, and that the results are really good.