mtPaint
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toggling layer visiblity also selects layer
Clicking the checkbox to show/hide a layer will also select that layer. Since the current layer is always visible, this forces you to select a different layer in order to see what the image looks like when that layer is hidden.
Unlikely that anything good could be done about that, considering the way input focus works. If I make the checkboxes unfocusable, it'll completely preclude using keyboard to navigate to them and toggle them - and that capability can be useful on occasion. And when they are focusable, their row is by definition getting selected when they receive focus.
As to current layer "always being visible", it is because you're staring at the wrong window. :) It is the view window that displays the composited image; even if the option to "show all layers in the main window" exists too, that is purely assistive.