I'm not suggesting Pfizer is up to something nefarious, just that the biomedical literature is littered with studies with N < 100 for the outcomes of interest and they don't replicate. The N > 40k in some ways is irrelevant if none of those participants have the processes in play. It's more like recruiting N >40k to get N=94 to study.
I'm also not suggesting with 90% effectiveness that there's probably no effect, just that my guess is a true value of 60% isn't outside the realm of possibility once you consider all the factors that could be in play besides the random sampling variation that's assumed by their tests.