Just some input – I found this thread as I was searching for a solution. Many of my clients with WP blogs integrated with their business sites are not happy that I can’t get the logo to represent them in the email notifications to subscribers when a new post is published.
This singular issue is the basis for them to request that I move away from the problem (Jetpack) and to another plugin even though everything else is working great. I am currently searching for another plugin with a similar functionality as Jetpack.
I have the Avatar set properly in the Reading settings and the favicon for the WP theme and everywhere else under the sun. There is nothing but frustration brewing when the branding for the site is thrown off by the wrong avatar in the blog notification emails.