Sorry for the off the cuff replies, that was from my phone. I was mixing what I read with my own conjecture. I was thinking originally that you were being paranoid, and after reading it does appear that this is a realizable concern, even though the probability of occurrence is low. I have been doing no chill for many years now and obviously have never contracted botulism. However one of the articles quoted a food safety expert as saying that this is an accident waiting to happen.
I did see a thread where someone thought that phosphoric acid was causing an off flavor but they didn't really have definitive evidence, they were just spitballing possible causes of a problem.
With regard to flavor stability my concern is that a water profile was targeted and brewed; then an acid is added which needs to be neutralized with something like NaOH, or CaOH. The problem now is that you have added a bunch of calcium or sodium to your existing water profile. Maybe this can be accounted for in the initial recipe design but it might also make targeting mash pH difficult, or may have other unknown affects. I have heard of off flavors from using large amounts of lactic acid so personally I am concerned about adding large amounts of weak acid to enact a significant pH change.
You mention that solubility would be a factor in neutralizing the acid, but I don't think so. LeChateliers principle says that as the base is reacted out by the acid the reaction would be shifted in the forward direction increasing solubility. We would have to worry about common ion effects though since we already have ions in solution from having set a target water profile.
Other considerations with regard to changing pH are the buffer capacity of the wort. If it is high then adding weak acid or base is only going to help in extreme quantity (which could cause flavor change), and can only be verified with a pH meter, which I do not own (not sure about you). The alternative is using strong acid, and strong base, but still may require considerable amount. I think that KOH would probably be the best base. A lot of us use campden tablets and K-meta to treat water for chlorine and there seems to be no concern for how this affects final ion concentrations. I don't know what acid would be best though, HCl would affect our final Cl- concentration and I don't think Br- and I- are good for you in significant doses. Also I'm not sure how to get it since lab supply stores won't ship to residential addresses.
So to summarize I think there are really three options if the wort is going to be stored for long periods of time.
A. Acidify and neutralize while accounting for the overall affect on final ion concentrations in the resulting beer. This would be best tested on two 1G batches. One no-chilled, the other ice bath chilled in the sink. Then fermented side by side and compared with a triple blind study and a decent sample size.
B. Bring the already no-chilled wort back up to 80C for at least 10 minutes to neutralize any toxin formed by the CB, then cool and pitch as soon as possible.
C. Keep the wort refrigerated until ready to use (based on the recommendation for baked potatoes).
The articles I read didn't say not to no-chill beer but did say that it should be pitched as soon as the wort is at or close to pitching temperature, and not to delay. It would be nice to get some data on the effect of hops and alpha acids on C. Botulism bacteria and whether or not high alpha beers would affect there ability to reproduce.
I have to admit I am still skeptical about how concerned we should be. Beer, mead, and wine has been brewed for centuries before wort chilling was invented. I would imagine they just waited until the wort was a reasonable temperature then stirred it with a stick inoculated with yeast. Granted they would presumably be doing this soon after brewing, but also were probably severely under pitching, and didn't have their wort in sealed containers while it was waiting to ferment.
I'm not going to worry about this too much since right now since it is winter and my stored wort is going to be sitting at near freezing in my garage until ready to ferment. However if I get bored I may try option A. above with two 1G batches. I think if I make a significant change to my brewing in the future it would either be to try to get the wort fermenting sooner, and if that failed to buy a heatstick form Bobby to use as a bucket heat and heat the wort in the jugs the day I plan to pitch.
Sorry for the novel.