@Giles A The only things I can see that don't adapt correctly are the TextField, TextArea, Bezel button and Listbox but I don't know if they're even supposed to adapt...
When you introspect these controls on their Mac side, you’ll find that there is a XOJTextField and a XOJTextView class, so they are basically native controls and should adapt to Dark Mode. But the TextFieldCell’s drawWithFrame:inView: method is overwritten, so that’s probably the place where the engineers could fix the behavior.
Labels could simply stay black because of their TextColor property being black usually. I think it would be best to address NSColor’s TextColor "constant" instead.
The only bigger deviations are obviously the Listbox and the BevelButton which are built on a view subclass. Again, the drawing routines should be changeable to use the system colors instead of default black and white.
Funny aspect: The Listbox headers under Mojave Beta are semi-transparent in a screenshot. They are pitch black on screen.