I'm a little nervous to comment... I hope this won't offend anyone...
IMVHO I think the clearest code is rminner's code.
IMVVHO The 2nd clearest is ... oh look over there, a spider ... *whispers* the original code.
IMVVVHO Both make it very clear what the 2 different cases are, and what to do for each of them.

I like to line things up to help highlight the similarities and differences, so I might write it like this:

sub id2path_new {
    my ($id) = @_;
    return '' unless $id;

    my $path = '';

    if ($id >= 1_000_000) {  $path = sprintf("%09d", $id);  $path =~ s
+#\A(.*)(...)(...)\z#$1/$2/$3#;   } 
    else                  {  $path = sprintf("%06d", $id);  $path =~ s
+#\A(..) (..) (..)\z#$1/$2/$3#x;  }
    return $path;
}
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