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All should be ready if you use this ModuleDependency:
[ModuleDependency(typeof(EPiServer.Web.InitializationModule))]
ContentReference.StartPage is resolved from the http request. See http://world.episerver.com/Blogs/Johan-Bjornfot/Dates1/2013/12/Multisite-feature-in-EPiServer-75/
You can in admin mode (under Manage WebSites) add host name '*' (wildcard host) to a site. Then that site will be returned as SiteDefinition.Current (and hence also ContentReference.StartPage) when a site can not be resolved from the request (either when there is no request or the host of the request does not match any site).
I need todo a few checks when ContentReference.StartPage is ready. Can I somehow hook up on that event?