RE: Product variant cost price
Yes I am afraid you have misunderstood.
The purchase price in the costing version is used solely for BOM Calculations, it is not referenced on any purchase order to my knowledge, you have to set trade agreements or use the purchase price for that. Now you have activated the cost price it will record costs in this manner against the item and cost in that manner, without it it does not.
PO and SO by variant is only from trade agreements. You only need to calculate the purchase price in the costing version (your inventory) to use in your calculations - purchase prices are defined by the vendor.
With the BOM calculation you can transfer this to the sales price of the item if you want.