Great question. There is plenty of benefit to adopting agile self-organization and allowing teams to select their tools. However, there are typically limitations imposed by the business. For instance, a business might not be able will enable each scrum team to roll its scrum solution. If the business is established, the more company has, the more restrictions and resistance. Even established businesses can change. Ask questions about an obligation if the team can justify the move.
Agile planning tools adhere to the same guidelines. A business might possess a complete Life Cycle Management software system in place. This solution might or may not include the agile component. However, the company might have the need (regulated industries, for instance) to demand that the design inputs or outputs are recorded in the software for their life cycle management. The company usually has to keep the teams satisfied and productive while staying in business.
I don’t believe there will be a black-and-white solution (unless you’re one of the very first developers at the beginning of a new company). Agile teams must embrace open communication. If the tools cause obstacles, the company must be aware.