Problem: WordPress MultiSite sends user signup mails from the main site. This is a problem when using domain mapping functionality as the sender is not the same domain as expected when creating a new user from a blog with another domain.
Solution: Change the default user notification mail with a filter wpmu_signup_user_notificationĀ from using the main network admin_email and site_name to the blog admin_email & blogname
https://gist.github.com/1331582
So this code has to be added to every individual (Child) multisite functions file or parent function file (can you point me to the exact file where to add this code)
On my Multisite (sub-sites) every site has its own subscribe to email form (but still the site admin gets notification from super-admin instead of the local blog/siteurl (the way you are doing for activation) would this code also work for that purpose as well ?
Late reply, I was at WordCamp Lisboa š
You can add it to functions.php or make a plugin and put it in mu-plugins.
This code would not fix normal notifications the way you describe. Maybe us some sort of smtp plugin and set it per blog?