Correct.
The quality and appropriateness of presentation and packaging materials used for proof sets is
not usually the problem. Hard sealed set cases
have to broken if you wish to do something with the individual coins.
There are quite a few articles on Google that explain the formation of spotting on silver bullion coins.
There are also quite a few articles to be found on how to remove them. Consider carefully before any of these removal procedures are adopted. I have never tried any of them - I don't collect proof bullion coins.
As far as protection of silver (in particular, proof), bullion coins is concerned, I believe the best way to preserve and protect them is to
enclose them in individual snap lock clear acrylic plastic capsules of appropriate size.
That way, it is still possible to handle the individual coins without gloves or further protection.
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Unfortunately, some of the spotting found on proof silver forms long after the product left the Mint. Research has revealed that one of the reasons for such spotting is an outcome of the annealing process, and Mints are well aware of this.
Perth Mint has taken some further experimental action in this regard, by striking proof coins in a laboratory clean air environment to reduce surface contamination problems, and has made adjustments to the annealing process, and further cleaning of the blanks after annealing.
All of this may well come with extra sale cost of their products.