Right, but the people making the argument about vaccines don't understand the principles, because they're actually the same!
1) a double blind RCT with a placebo control is a very good way to understand the effectiveness of a treatment.
2) it's not always ethical to do that, because if you have an effective treatment, you must use it.
Even without a placebo control you can still estimate both FN and FPs through careful study design, it's just harder and has more potential sources of error. A retrospective study is the usual approach. Here, the problem is they only included true positives in the retrospective study, so they missed the opportunity to measure false positives.
And the problem with -that- is that it's very easy to have zero false negatives if you always say " it's positive". Almost every diagnostic instrument has something we call a receiver operating curve that trades off false positives for false negatives by changing the sensitivity for where you decide something is a positive. By omitting the false negatives, they present a very incomplete picture of the diagnostic capabilities.
(In medicine you will often see the terms "sensitivity" and "selectivity" for how many TPs you detect and how many TNs you call negative. It's all part of the same type of characterization.)
The two points you raise with regards to why vaccine or similar studies may be treat special, it doesn't replace the loss of data when a double blind study with a control or make estimates based on modelling indicate anything more than correlation.
We may broadly agree that submitting a control group to a placebo treatment for a particular disease is immoral, but that doesn't mean such a study isn't necessary to prove out the efficacy or safety of the treatment. As for modelling, for example trying to estimate FN and FP, it can only ever indicate correlation at best and will never indicate likely causation.