Multidomain + Clean URLs + WOL needs a lot of workarounds. We have to work on this anyway, because I'm not even sure default WOL had been working correctly anymore. Not reported because I started working on this (and thus broke it even more) before seeing if it was working in the first place. Either way, this requires a complete rewrite of the WOL handling (a total of 6 plugins, not just at the usual online_location_xxx hooks). We are currently undertaking this.
We also partially rewrote multidomain handling elsewhere. The vault_multidomain_urls hook has been removed and instead replaced with a parsing of the $vault->misc['multidomainurls'] object. Using this as a domain map enabled the additional of new features, including forwarding if the correct domain is not visited when viewing certain namespaces. Because the map is an(other) "advanced" feature, it is only accessible via vBulletin's plugin system.