Embora seja sabido que a janela de login oculta todas as contas de usuário com IDs abaixo de 500, parece o ID do usuário 1000 também está oculto :
The next option is to set the user's ID to 1000. In OS X, an account with UID 1000 will not show at the log-in window, so you can select one to use and set its ID so it will not display. To do this, go to the Users & Groups system preferences, authenticate, and then right-click an account to select the advanced options. In here, you should see a set of fields with some details about the account, such as its home folder, name aliases, and its UID. Simply change the UID value for the account to 1000, apply the changes, and the account should no longer show up at the log-in screen.
Sua única maneira de sair disso é provavelmente ajustar o seu Linux para os IDs de usuário do Mac, ou alterar ambos os sistemas para, por exemplo. 1001.