Functional and conditioning exercises both have benefits in different areas and can be used together to create an efficient workout routine with benefits for many activities.
Functional exercises are great to use when doing workouts that need to be completed in a short amount of time, for example, circuit training programs where each exercise is done for a certain amount of repetitions.
Functional exercises are also used to increase coordination and balance which benefits activities such as sports and yoga where balance is required.
Conditioning exercises can be done to increase muscle strength and endurance, especially when doing high repetition or high resistance workouts such as weight lifting or bodyweight workouts that require a lot of muscle endurance.
Conditioning exercises can be beneficial for any type of athlete by increasing power and control for that sport.