The OP's script captures both STDOUT and STDERR, but plain backticks will only capture STDOUT.
As a demo, I used a script like this:
#!/usr/bin/perl
print STDOUT "hello\n";
print STDERR "world\n";
If you run it on a bash cmd line you get both lines of output as you would expect. If you call via perl backticks then only "hello" is captured, and "world" is still sent to stdout.
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