This should absolutely be a feature of Business Central, as it is in Finance and Supply Chain. It is a bit frustrating to think that a customer will use stockkeeping units exactly as intended and there is no way to possibly run an independent cost roll for the variant, or produce the variant at it's own standard cost that does match the item. This also applies to other cost environments besides standard. For example, in a FIFO environment the variant should be creating it's own item ledger entries and having it's own cost capitalized and expensed out correctly, rather than blending item ledger entries and cost for all variants of an item.
We have this issue as well with several clients. Another common example is pack size conversions. Let's say you have a primary item in the plan group that is called out on the formula in eaches and the alternate item's base inventory unit is eaches. The pack sizes of the two items differ and we twice as much of the secondary item as the first. MRP will short the planned production order by half of what's needed for the alternate item.
This is a mandatory functional requirement in companies that have used palletizing in the production or purchase of goods. It took more than 2 months to develop the functionality, and the customer is dissatisfied with the fact that he paid extra for the the basic functionality that was not in the system standard.