You have to create your custom race first as an opponent - or open it in the opponent window after you've created it - and edit the alignment. It's the only thing you're not able to do normally in the custom race window.

To create my good-aligned custom race the Herans, for example, I created my custom race, used the Save button, then used the Back button to go back to the Race Selection window, selected one of the canned races, went all the way to the Select Opponent window, selected my custom race, clicked Edit, changed their alignment, hit Save, then went all the way back to Race Selection and started the game from there.

Kind of a pain, but it doesn't involve editing the file manually, so I don't consider it part of the "Advanced Race Customization" controversy.