When you know that you have a problem at hand, where template matching would be a better approach, you can use that. However, it could be that more complex tasks (where usually CNNs are used) for which it's not immediately obvious that this capability is required, would also benefit from this capability.

Ensembles are a practical solution, but it's kind of ugly. Remember, this is research into limitations and capabilities, not about solving particular tasks. Once the issue is identified it can be tackled and the resulting model may be nicer and more elegant than an ensemble.