Eu acredito que quando você executar java --version , você obterá java 9 , mas qual é o seu padrão. Agora update-alternatives apresentará ao sistema várias opções para programas aplicáveis e indicará qual é a opção padrão quando não for selecionada manualmente pelo usuário, por isso as opções auto seen e two para java 9.
Trecho de man update-alternatives :
update-alternatives creates, removes, maintains and displays information about the symbolic links comprising
the Debian alternatives system.
It is possible for several programs fulfilling the same or similar functions to be installed on a single sys‐
tem at the same time. For example, many systems have several text editors installed at once. This gives
choice to the users of a system, allowing each to use a different editor, if desired, but makes it difficult
for a program to make a good choice for an editor to invoke if the user has not specified a particular prefer‐
ence.
Debian's alternatives system aims to solve this problem. A generic name in the filesystem is shared by all
files providing interchangeable functionality. The alternatives system and the system administrator together
determine which actual file is referenced by this generic name. For example, if the text editors ed(1) and
nvi(1) are both installed on the system, the alternatives system will cause the generic name /usr/bin/editor
to refer to /usr/bin/nvi by default. The system administrator can override this and cause it to refer to
/usr/bin/ed instead, and the alternatives system will not alter this setting until explicitly requested to do
so.
Em outras palavras, ele diz que você tem três opções para java e que uma dessas opções sempre será usada em circunstâncias normais.