Você pode alterar AuthorizedKeysFile para algo fora do diretório inicial, por exemplo, /etc/ssh/keys/%u/authorized_keys . Então as chaves estarão disponíveis antes de /home/%u ser montado.
Na página do manual de sshd_config :
AuthorizedKeysFile
Specifies the file that contains the public keys that can be used
for user authentication. The format is described in the AUTHO-
RIZED_KEYS FILE FORMAT section of sshd(8). AuthorizedKeysFile
may contain tokens of the form %T which are substituted during
connection setup. The following tokens are defined: %% is
replaced by a literal '%', %h is replaced by the home directory
of the user being authenticated, and %u is replaced by the user-
name of that user. After expansion, AuthorizedKeysFile is taken
to be an absolute path or one relative to the user's home direc-
tory. Multiple files may be listed, separated by whitespace.
The default is ''.ssh/authorized_keys .ssh/authorized_keys2''.