Seriously, despite it being more likely for an unvaccinated person to have serious adverse effects than a vaccinated person, overall an unvaccinated person is still more likely to not have serious adverse effects than to have them. Regardless of the relative difference, the absolute odds is what the phrase is referring to.

The "odds being stacked against" something declares that one is very likely to experience an unfavorable outcome, stacked suggesting a strong disadvantage.

Again, I fully agree with all of your points, you are correct in all points except the usage of that particular phrase.