The line:

foreach my $line (@array) {
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assigns the value from the next item in @array to the variable $line. I find this makes it eaiser to see what you are doing, rather than using $_, which I find non-intuitive.

Yes, you are correct, that next line of code skips anything that starts with a #, so that only lines from your file that are not comments are inserted into the array that you are intending to send to the output file.