Have you tried going to Settings > General > Reading, and choosing Open in New Tab? A double-click will give you a message window that's the full size of your Thunderbird window. I think you might have to open View > Layout and uncheck Message window first. I use Vertical layout; no message window, Cards view of the message list, and my messages open full-window in a new tab with an X on the top right for when I'm finished with that message, or I can just click the Inbox tab and the message list will appear, without closing the previous message. Works beautifully.

I have the same problem. I saw a solution to it by editing the #threadPane min-height value in the chrome.css file That solution seemed to work for some people but did not work for me. IMO the Developer should fix this by allowing whatever size the user wants.