You can and should specify the default email from address in Administration Menu > Site Settings
That "may" solve the spam filter problem. It can also depend on what mail server you are using, some spam filters do a reverse lookup to make sure it was sent from the correct mail server.
Unfortunately, at the moment the subject for the registration email is not configurable, it will just use the site name, so I don't know why it is blank.
The body of the email is configurable in the sense that it can be localized, but not really customized. It will use the text template file /Data/MessageTemplates/en-US-RegisterConfirmEmailMessage.config
if the default culture as configured in Web.config is not en-US, it will look for a file with the current default culture.
Its not really customizable because next time you upgrade the files will be overwritten and any customization would be lost.
Hope it helps,