If you’re purchasing transport services in Scope 3.4 and 3.9 (in $), that monetary emission factor includes provisions for warehousing emissions. If you’re using physical shipping data in scope 3.4 and 3.9, you should include warehousing energy use separately in scope 1 and scope 2 under your facility 'Brand Name' Operations.

This may require that you reach out to your distribution and warehouse contractors to ask how much of their total energy and fuel use is attributed to your company.