I have Automessage installed and Network Activated in WP Multisite.
On a subsite I created a User Level Automessage with the following;
blogname = %blogname%
blogurl = %blogurl%
sitename = %sitename%
siteurl = %siteurl%
When I receive the email the blogname and blogurl is showing up as the primary site, not the site the email is coming from. sitname shows up as the Network site name and siteurl shows up as the primary site.
Note: I also run WP Better Emails and the Header is set to %blog_name& and that does come through correctly as the subsite name.