Got mine, boxing was fine. Largest silver proof set I have in my collection. There is a spot on the ASE but I am not experienced/qualified to tell if its on plastic or coin. I will assume its on the plastic, unless more people say there is an issue with the ASE's in the set.
Impossible to say without seeing it, but ASE proofs are known to get spots and do sometimes have them already when delivered
The only reason to get the set is for the ASE. If it doesn't please you consider returning and replacing. They are back on sale at the mint.
There are subtle differences depending upon which mint produced the coin. Take the 2011 bullion issue in the anniversary set. They were made at two different mints without mint mark. But, if you look at enough oft them, there are differences in the finish.