Unless someone has developed a bolt-on app for this I really doubt there is any way of controlling returnable by-products in Dynamics 365 for Financials (or in any other comparable ERP system).
In my experience (with another system being installed in a dairy, where they were sending out crates of milk in glass bottles for door-step delivery) much of this is kept 'off system'. The cost of the containers being sent out has to included in the price of the milk, recognising the likely lifespan of the container, so that it is not a crises if every bottle and crate is not returned. A glass milk bottle in the UK on average seems to last 8 door-step delivery cycles, therefore the accountants at the dairy included 1/8th of the cost of a glass bottle in the price of each pint of milk.
The BOM for the pint of milk (or bottle of beer) obviously needs to include the bottle, so it needs to be an item in inventory and therefore have a quantity on hand. But, in the dairy situation we just back-flushed the bottles and allowed stock to be over-drawn. It would be someone's job just to keep a visual eye on stock levels of glass bottles (taking into account new ones on hand and used ones returning through bottle washing) and, from time to time, order in a few more. Similarly with plastic crates.
If you want closer control than this you'd probably be looking at bar-coding every glass bottle and crate, which just isn't practical...
The situation would be different with barrelled beer, where the keg is expensive and valuable and the beer inside cheap. Here bar-coding or uniquely numbering the kegs might work, but again I think the control system for the kegs would be something outside the D365F ERP system.
[Just my 2p worth to start a conversation; probably someone will be along with better ideas shortly. I don't work for Microsoft and have limited knowledge of D365F.]
