How to change WP Email Templates without touching the code

Hello everyone,
We already installed a few email plugins to change the email design/template, but they only seem to work for some of the mails..
Most of the mails look like this: https://teamwpde.files.wordpress.com/2014/02/wpcom-abo-mail_v3.png (for example the subscription mail, the follow-comment mail etc.)
HOW can we change the Design of that emails? At least we want to display our logo instead of the wordpress logo on the top left. If its possible is there a way to change that without overwriting existing php functions of wordpress?

Thanks in advance