There is no such limitation, if you do it right:

$ cat foo.pl
#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

if (@ARGV){
    print Dumper \@ARGV;
} else {
    system $^X, $0, "a\nb";
}
__END__
$ perl foo.pl
$VAR1 = [
          'a
b'
        ];
[download]

You can see that the script calls a copy of itself, and both lines of a\nb are passed correctly to the second copy (tested on Linux).

Which makes me think that you're doing something wrong.