The notion of domain and cron

When using DA along with modules that do send mail via cron (subscriptions, auto_expire, scheduler, etc...), the notion of domain is lost. All links in the e-mail messages will point to the main domain, often resulting in "page not found". I understand that this is the result of cron being treated as a "special page", and for a reason. Is there any workaround for this problem? Does DA exposes information that would make it possible for other modules to solve it? Thank you.