My issue occurs upon dereferencing the array. my @unfilteredOutput = @$outputRef;

That not (just) dereferencing the array, it is copying it. Effectively doubling your memory usage. So don't do that.

Anything you can do with @unfilteredOutput, you can do using $outputRef (using a slightly different syntax), without having to copy it first.

For example, you might iterate the elements of @unfilteredOutput like this:

$_ += $somevalue for @unfilteredOutput;
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You could do the same thing without having duplicated the memory using:

$outputRef->[ $_ ] += $someValue for 0 .. $#{ $outputRef };
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And for your example, you can do:

my $total_size = total_size( $outputRef );
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Which will give you the same number, but will avoid having to duplicate it all first.

It seems like you need to read perldsc.