Yes, all MTB activities are taken into account when you are working towards a JOIN training goal. But it does make a difference what sort of MTB efforts you do. If you ride dirt tracks/fire roads, etcetera, then it's more or less normal endurance training. However, if you are really shredding purpose-built
MTB courses, the riding will most likely be a lot more technical, explosive, and harder and it will become difficult to focus on maintaining certain HR or power levels. Instead, you will have to rely more on feeling. However, the HR or power levels will still tell JOIN how hard it was and will be taken into account in the plan accordingly.