See perlsyn. If you prepend a #line comment in front of the file, Perl will adjust the error message accordingly:

sub include {
    my($filename) = @_;
    open my $fh, '<', $filename
        or die "Couldn't read config file '$filename': $!";
    my $content = do { local $/; <$fh> };
    my $r = eval { join "\n", sprintf( qq(#line 1 "%s"', $filename ),
                              $content };
    ...
}
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