Correct me if I'm wrong, but isn't gnome-tweak-tool intended for Gnome3? Gnome3 is GTK 3 while Mate is GTK 2 (resurrected).
Which also means a GTK 3 theme will not work correctly in Mate.
And my question is... am I correct to assume the latest release of Transmission will not use my GTK 2 theme
Transmission use GTK3 themes, whereas MATE applications use GTK2. If you choose a theme that doesn't have GTK3, those apps will end up like that.
*I reread your post and believe you answered that... I only have two programs not using my current theme, which are Transmission and K3B (which I know K3B is KDE based and does its own theme).