Do I need to account for transport of purchased inputs (e.g. feed) or final products to/from the farm?
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? We generally advise a cradle to farm-gate approach.
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 purchased livestock feed, it's important to include the transportation of this feed to the farm as this is not included in the GFLI emission factors. This aspect is essential for a complete cradle to farm gate approach, as transport emissions will contribute to the overall footprint of feed. See also: Can I contribute to GFLI's transport database initiative?