Template overrides are only for templates?

Can we override only files in the Template folder or other files too?

If I want to override a controller (example)… do I have to duplicate it into my own plugin controller (as a controller) and work from there… or can I just do a template override ?

This is OO programming. Your Controller can extend/derive from the relating controller.
Of course, you could clone and extend the code, but this is IMHO bad practice.

class ConfigController extends \Kanboard\Controller\ConfigController {
   //  usual implementation

class MySpecialConfigController extends ConfigController {
   // additional stuff goes here
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