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I think you may be unsetting some things in your alterRoutes method doing it the way you are. (However, I can't tell if or why that's happening after looking at Route::addDefaults().)

I'm doing the same thing for a media entity's route. My alterRoutes method is a little different - I'm using Route::setDefault().

public function alterRoutes(RouteCollection $collection) {
  if ($route = $collection->get('entity.media.canonical')) {
    $route->setDefault('_controller', '\Drupal\my_module\Controller\MyController::view');
  }
}