Isn't better this

Debugger::setLogger(new StreamLogger);
Debugger::enable();

than this?

Debugger::enable(Debugger::DETECT, new StreamLogger);

The issue is that in Nette you're never actually calling Debugger::enable(), because there is $configurator->enableDebugger(). So, the actual comparison is

Tracy\Debugger::setLogger(new Tracy\StreamLogger('php://stderr'));

$configurator = new Nette\Configurator();
$configurator->enableDebugger();

vs.

$configurator = new Nette\Configurator();
$configurator->enableDebugger(new Tracy\StreamLogger('php://stderr'));

When I think about it now, the logic could be moved to Nette\Configurator – but it would create disparity between Tracy\Debuger::enable() and Nette\Configurator::enableDebugger() signatures.

create disparity between

It does not matter.