A minimum stock quantity should be irrespective of anything else, i.e. not depend on a production plan, relationships between other components, or minimum stock quantities of other components. It is a safety check to ensure you always have some quantity of a typically critical part always on hand, e.g. a spare full reel of a hard-to-get component, a spare roll of kapton tape, a spare box of 4-40 screws, etc.
Production planning, or MRP, is an operational system, it takes care of questions like "what do I need to buy in order to build quantity X of assembly Y by date Z. An MRP system takes a bill of materials with supply chain details for purchasing individual parts (with leadtime and quantity price breaks), and desired production quantity and delivery date, and using the component purchasing lead times (and possibly production workstation process times), and tells you when parts should be bought, when, and in what quantities, for you to achieve your production plan.
What is the best practice will depend on what you want to do. Do you want to ensure sure you have some minimal quantity of a critical part always on hand, or do you want to plan the purchasing to build a product based on a sales or production plan?
You can adapt these concepts to your own situation. For example, if you manage minimum stocking quantity of parts but do not use MRP, you could configure appropriate minimum stock quantities that would be sufficient to build some number of finished assemblies.
With relatively small quantities of a relatively small number of BOMs, it might be more convenient and efficient to simply treat each board build as a completely separate production job. Planning will be simpler and you can use simpler tools if you don’t have to take into account whether a part is used on more than one BOM. Separate jobs might even be preferred if the time it takes you to do production planning is greater than the cost savings from buying in greater quantities or issuing fewer purchase orders.
Designers often spend a significant amount of time finding the best part, or the best supplier with the best price, without considering their own time may be the most expensive input to the manufacturing cost - or the opportunity cost of not using that time for something of greater value.
Does that help?
Cheers,
Dale