I think you can defend it strictly for transporting the partial raw materials back to the warehouse, kind of the same practice as the warehouse picker grabbing cases for a small production run. When an auditor sees previously opened partials on a pallet, they're still going to ask questions like "Were those boxes open together on the pallet before being resealed?" If they were open on the same pallet at any time, auditor is going to be able to make a case that it's unacceptable.
But then as soon as forklift driver sets that pallet in a home unattended, auditor is going to flip their lid over a comingled pallet placed into any storage type situation (even temporary).
Not sure which scheme you might be under, but SQF as an example has no leeway for this. I've taken hits from auditors for them finding a completely sealed pallet of milk containing ingredients in pallet racking directly above a completely sealed pallet of soy ingredient.
2.8.1.3 Provisions shall be made to clearly identify and segregate foods that contain allergens. Segregation procedures shall be implemented and continually monitored.
Some guidance found here: SQFI | Allergen Management
a. Instructions for the receiving and operational staff on how to identify, store, and keep separate non-allergenic materials and any materials known to contain allergens shall be documented. SQF sites must identify all allergenic ingredients at receipt, and store them separately from non-allergenic materials, and from materials containing other types of allergens. Staff involved in receiving and storage must be fully aware of the presence and risk of allergens and the storage procedure. All ingredients must be clearly labeled with the name of the allergenic substance and must be stored and transported to avoid spillage or leakage onto other non-allergenic materials.