There may be some switch in Perltidy so that it doesn't do the indent in the middle, I haven't found an answer yet.

The documentation says:

       -isbc,  --indent-spaced-block-comments
           If there is no leading space on the line, then the comment will not
           be indented, and otherwise it may be.

And thus we see:

$ cat 11117714.pl 
sub foo {
    my $i = shift;
####################
# Name or Description of Code Section
####################
    return ++$i;
}
$ perltidy -npro -isbc < 11117714.pl 
sub foo {
    my $i = shift;
####################
# Name or Description of Code Section
####################
    return ++$i;
}
$
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