As I stated above, there are design issues. By altering the userchrome.css file you can insert own style rules fixing them. As inserting them for all users causes a risk of breaks in rare cases, I do not include fixes for that, that's the theme's authors buissness. Maybe you want to contact the author of your favorite theme and ask him/her to support this extension?
Missing toolbar divider line in default theme on Windows XP or earlier
This fix was provided by RDL. Thanks!
#mail-bar3 {
border-bottom-style: solid !important;
border-bottom-width: 1px !important;
border-bottom-color: threeDShadow !important;
}
#tabs-toolbar {
border-top-style: solid !important;
border-top-width: 1px !important;
border-top-color: threeDHighlight !important;
}
Transparent menu bar with the default theme
This fix was provided by rctgamer3. Thanks!
@media all and (-moz-windows-compositor) {
  #mail-toolbar-menubar2 {
    background: transparent !important;
  }
  #messengerWindow:not([sizemode="maximized"]) #mail-toolbar-menubar2 {
    margin: 0 1px !important;
    border: 0 !important;
  }
  #menubar-items {
    background-color: rgba(255, 255, 255, .5) !important;
    border-radius: 4px !important;
  }
  menubar > menu:-moz-window-inactive {
    color: ThreeDShadow !important;
  }
}
Background for the Toolbar with the default theme
This fix was provided by CryingByte. Thanks!
#mail-bar3 {
  background-color: #e9eff5 !important;
}
Remove empty space with Oxybird2 theme without custom toolbars
This fix was provided by uyar. Thanks!
#mail-toolbox { display: none !important; }