Seeing this on linux/trunk. Likely related to spaces toolbar, or started showing up around the same time at least.

When a message needs maybe 2-3 screens of rolling or so (at least), I can no longer scroll to see the bottom content of that message, because the window "ends". The status bar on bottom is no longer shown, and the spaces toolbar bottom controls (<- and settings) are also off the bottom of the screen.

Using the window controls to go from a custom size to a smaller size seems to reproduce it pretty well. The problem shows for all messages, it's just more of a problem for the longer ones - for the rest it's just the missing status bar, and somewhat odd ending of the window.

Thanks for the report, I'll take care of it.

I see that, when I reduce the height of the window, the spaces toolbar doesn't shrink when the top and bottom buttons meet and close the gap between them, causing the rest of the UI to be pushed outside the application window frame.

This happens regardless of the length of the message.
Is this what you were referring to?
I can't seem to reproduce this issue in any other scenario other than making the window height very very small.
Would you be able to add a screenshot or screen capture if you can reproduce it in any other situation?

This is what it looks like. I noticed now, without the today pane the problem doesn't show at least in this example. Toggling it with F11 makes the problem show/not show.

I'm very confused by this as I'm not able to reproduce the issue.
The only thing I could think of that might be affecting it since the introduction of the spaces toolbar is the styling of the body as display: flex rather than the default display: -moz-box.
It seems that -moz-box is kind of a flexbox emulation, so I'm not sure what I did changes anything.

Let me know if the problem is solved with the uploaded patch.

Fix Overview

This patch removes the custom styling of the body added during the Spaces Toolbar implementation.
The styling of making the body a display: flex was introduced in order to properly align the vertical toolbar with the horizontal messenger container.

Doing so caused issues to the application window, specifically the inability to properly resize and wrap/clip its child elements inside of it.

The body, and the child element #messengerContainer should keep the default attribute of display: -moz-box;. Even tho -moz-box is an emulation of flex, it behaves differently for the application window.

Pushed by alessandro@thunderbird.net:
https://hg.mozilla.org/comm-central/rev/7150d532907b
Do not change styling of the main body to prevent wrong sizing of the main application window and its child elements. r=mkmelin