A configuration that doesn't change HOME
or works with symlinks can be found in my answer http://emacs.stackexchange.com/a/20508/934https://emacs.stackexchange.com/a/20508/934. With this configuration you can change the user-emacs-directory
by setting an environment variable:
EMACS_USER_DIRECTORY=~/.emacsenv.d/spacemacs emacs
and this even works with the daemon.