I laid out the argument that science is what scientists do here Philosophical assumptions underlying science
One-off or near unique events can still be investigated by science. Chixulub, gamma ray bursts, the big bang - we study that and are as 'far' from it as it's pissuble to be, in space & time. There was a first ever dissection of a whale done with science in mind. A less experienced scientist isn't necessarily less scientific - in fact almost every Nobel Prize was received for work done before age 30.
if the answer is yes, then how is they relatively confident that they don't miss something (the unknown unknowns)?
We develop domain-specific toolboxes. Consilience or convergence of evidence is a good start. Correcting for cognitive biases, with tools like double-blind trials, might be needed. Galen caused over a millennia of medics to ignore their own eyes during dissections, because he had nit dissected humans, only pigs & chimpanzees &c.
I think of the detection of gravity waves as a masterclass in how science is done. Each source of noise was systematically minimised, given the budget, with steps like damping, multiple separated detectors to eliminate noise, and error bars chased to below the signal range (though in fact, thus scale was unknown).
In the whale example, there are clearly transferable skills from dissection & other surgical procedures. Literature may indicate key whale-specific issues - for rabbits I think the gall bladder should be removed quickly or it 'taints' the meat, which might be relevant to investigations. Sperm whales alone produce ambergris, which might warrant specific investigation in that case. Whale-strandings have focused on ear damage, which has required developing more detailed knowledge of the minutiae of dead healthy whales - it's thought military radar has been causing deafening sound bursts, resulting in certain microscopic air bubbles, causing pods to flee the water. There's always going to be the cutting-edge of research doing new techniques, and work-a-day routine science - but the boundaries of both continuously expand.
There's a whole deeper level about hypothesis generation & falsifiability, creating tractable abstract models, scientific paradigms, but that doesn't seem like what you are asking. It seems like you are trying to get at something deeper that you haven't made explicit..
I think the summary is, being better able to review methodologies, and think through unknown unknowns is what we call being a better scientist. Often before the science is done, we don't know who is good, so we use proxies like exams & interviews. But the good science of better doing these things, results in noteworthy insightful science, and we try to elevate those who can do that to supervise & teach.