system uses the shell when you call it with one argument. It doesn't do that when you call it with a list. The Perl Cookbook suggests code like this:

my $status = system($program, $arg1, $arg2);
die "$program exited funny: $?" unless $status == 0;
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I would expect the array to flatten into a list in your last example, but I wouldn't expect a list to become a single item. Which error message are you receiving?