If I understand things correctly, the preferred way to add stuff to
Info directory search path is using `Info-directory-list', e.g.:
(push "~/my-info-dir" Info-directory-list)
or:
(setq Info-directory-list (append '("dir1" "dir2"
"dir3") Info-directory-list))
This works in .emacs because Info-directory-list is autoloaded rather
than set in info.el. The documentation says:
The first directory in this list, the "dir" file there will become
the (dir)Top node of the Info documentation tree. If you wish to
modify the info search path, use `M-x customize-variable,
Info-directory-list' to do so.
The last sentence is IMO wrong: if you change the value of the
variable, you will completely override the autoloaded defaults. This
means that if the autoloaded stuff changes, e.g. by installing a new
package, the new values get ignored.
Info-directory-list should not be customizable at all.