The $wgConf variable is not necessarily configured; in fact, it typically isn't in single-wiki environments. WikiLookup is entirely based on $wgConf, so it will claim that there are no wikis, if $wgConf is empty. This is obviously wrong. In that scenario, it should just use the current wiki ID available via WikiMap. Patchdemo's CentralAuth config basically does something like this.
I also briefly considered whether this should be a core feature (i.e., set $wgConf after loading LS.php if still empty), but that increases scope and I'm not sure if we should do it; see also T212739.
