syspaths should be considered as constants to provide default values in case no configuration is provided. They are only evaluated on install time.

About respecting `root_dir` if no tweaking was done at install time, it simply [should respect it](https://github.com/saltstack/salt/blob/develop/salt/syspaths.py#L55).

Again, at startup, nothing in syspaths is "evaluated", [besides some minor stuff](https://github.com/saltstack/salt/blob/develop/salt/syspaths.py#L44-L54).

Did I make any sense?