There is a strong bias with many Agile practitioners about the need for a culture and mindset change with respect to Agile. I see the same stance from people in the business community when they talk about innovation. I’m sure you’ve seen many posts and forum discussions about how culture will eat your strategy for breakfast. This makes perfect sense for people who have their biases confirmed by these statements. For others though, changing culture and mindsets starts with more well defined processes, because they believe better processes will help them.
This speaks to the utility of the opinionated and feature bloated/loaded apps like Jira and Rally vs the more direct approaches such as using a whiteboard or apps like Trello and Cardboard.
Provided a strong management buy-in, coupled with continuous access to the insight and guidance of a trusted and empowered coach, an organization stands a great chance to succeed in their Agile Transformation with Lean or Agile only tools. However, since this isn't often the case, some of the familiar metrics and terminology, although not necessary, may somewhat reduce the anxiety of the transformation, and serve as a bridge between the old and the new. Also, the opinionated, prescriptive manner in which some apps expect to be used, may highlight incompatibilities with the old way, and suggest areas for modification and improvement.
On the other hand, the artifacts from the command-and-control era may just drag people back into the old mindset, and serve to preserve the old culture. Moreover, the uncompromising bulldozerlike rigidity of these apps may interfere with the developers' quest for mastery and autonomy.