Input is overridden by navigation input in Common UI. How to override?

The way I managed to work around this issue is to create a subclass of FNavigationConfig and to set it using FSlateApplication::Get().SetNavigationConfig(NavigationConfig);.
In my subclass, I overrode some methods such as virtual EUINavigation GetNavigationDirectionFromKey(const FKeyEvent& InKeyEvent) const override; that returns EUINavigation::Invalid when I disabled navigation.
You can also define your “mappings” for instance, the default is:

FNavigationConfig::FNavigationConfig()
	: bTabNavigation(true)
	, bKeyNavigation(true)
	, bAnalogNavigation(true)
	, bIgnoreModifiersForNavigationActions(true)
	, AnalogNavigationHorizontalThreshold(0.50f)
	, AnalogNavigationVerticalThreshold(0.50f)
{
	AnalogHorizontalKey = EKeys::Gamepad_LeftX;
	AnalogVerticalKey = EKeys::Gamepad_LeftY;

	KeyEventRules.Emplace(EKeys::Left, EUINavigation::Left);
	KeyEventRules.Emplace(EKeys::Gamepad_DPad_Left, EUINavigation::Left);

	KeyEventRules.Emplace(EKeys::Right, EUINavigation::Right);
	KeyEventRules.Emplace(EKeys::Gamepad_DPad_Right, EUINavigation::Right);

	KeyEventRules.Emplace(EKeys::Up, EUINavigation::Up);
	KeyEventRules.Emplace(EKeys::Gamepad_DPad_Up, EUINavigation::Up);

	KeyEventRules.Emplace(EKeys::Down, EUINavigation::Down);
	KeyEventRules.Emplace(EKeys::Gamepad_DPad_Down, EUINavigation::Down);

	// By default, enter, space, and gamepad accept are all counted as accept
	KeyActionRules.Emplace(EKeys::Enter, EUINavigationAction::Accept);
	KeyActionRules.Emplace(EKeys::SpaceBar, EUINavigationAction::Accept);
	KeyActionRules.Emplace(EKeys::Virtual_Accept, EUINavigationAction::Accept);

	// By default, escape and gamepad back count as leaving current scope
	KeyActionRules.Emplace(EKeys::Escape, EUINavigationAction::Back);
	KeyActionRules.Emplace(EKeys::Virtual_Back, EUINavigationAction::Back);
}

But the engine also offers an alternate nav config with a subclass defining its own rules (and a good place to learn more about the Navigation config):

FTwinStickNavigationConfig::FTwinStickNavigationConfig()
{
	bTabNavigation = false;

	KeyEventRules =
	{
		{EKeys::Gamepad_DPad_Left, EUINavigation::Left},
		{EKeys::Gamepad_DPad_Right, EUINavigation::Right},
		{EKeys::Gamepad_DPad_Up, EUINavigation::Up},
		{EKeys::Gamepad_DPad_Down, EUINavigation::Down}
	};
}