This depends on the scope you have defined for your assessments. Do you want to determine the emissions till the farm gate or e.g. till processor? Livestock feed, compost or other heavy inputs transported to the farm and used in production should be included.
For fertilisers, the tool does not automatically include transport emissions, as the location of production is often not known. Good practice, however, may be to also include the transport from your direct supplier. For feed items, the data includes transport from point of production to the Netherlands using a global average. You may want to include the transport from your direct supplier to your farm, which would provide a good estimate for feed items.