copy my separate array into a row of my array-of-arrays

I'd point explicitly out that there is a difference between taking a reference and copying the data within the array:

# Here, changes in @SeparateArray will be "seen" in 
# $MyAoA[$i] too
$MyAoA[$i] = \@SeparateArray;
pop @SeparateArray; # $MyAoA[$i] affected, too

# Here, $MyAoA[$i] and @SeparateArray are somewhat
# independent, even if they may share common elements
$MyAoA[$i] = [ @SeparateArray ];
pop @SeparateArray; # no change to $MyAoA[$i]
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This is something that remains somewhat "implicit" in your answer, e.g. when you talk about how to copy an entire array-of-arrays.