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There is a bug in hook invoke or I think it is. If it is not I think this should be included as a feature in next release.
The problem is following:
When you call the function
$extra = domain_conf_api(TRUE, $settings); you do not pass the current loaded domain ( current arg(4) ). In this function you are invoking the hook_domain_conf() with parameter current domain that is actually a global variable so it can be accessed everywhere and I personally cannot see why we need this. So if we pass the loaded by menu system domain parameter to domain_conf_api() and after that we pass this variable to module_invoke it makes much more sense. I've made a patch for this.