After evaluating the situation, we decide to keep the current behavior, as under some situation, the symbolic link need to be solved early to avoid other troubles.
And I think there is a easy solution to your problem. If you intended to use a file or directory beyond the $VH_ROOT, then avoid using $VH_ROOT directly in that configuration. For example, if you change log path configuration from
It will do what you want. The same for the User DB location configuration.