I discovered it by accident really.
I started from your solution to change the footer background color by editing MessageViewFooter.qml. In the folder /usr/share/jolla-email/pages I grep'd "MessageViewFooter, to see what comes up, and found that it’s used as a class in HtmlViewer.qml. I also noticed a file named MessageViewPullDown.qml, which I figured was the class for the pulley menu, rather than footer buttons. As it was not referenced anywhere else, I figured I would just add an empty block to see what happened. That’s all really 
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To be honest, I have no idea why it works haha !