You effectivly embed your here-document into another here-document with results in an extra newline.

Take this code:

#!/usr/bin/perl -w
use strict;
use warnings;

my $code=<<"END_MSG";
line 1
line2
END_MSG

sub foo{
return $code;
}

print "before calling\n";
print $code;

print "after calling\n";
print foo();
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When you run this you'll see there is no extra newline - so calling a sub does not magically add one.

But what you do is to embed the $code argument in yet another here-document which is where your extra-newline comes from.