Ok so I found out how it works.

In product.product there is a smart button "Cost Analysis". This functionality is calculationg actual cost of: BoM+operations+scrap. However, in mrp.bom there is a another smart button "Structure & Cost". This one is calculation cost of: Bom+planned operation. The latter is also the one used for product cost and inventory valuation.

Hence, my problem wasn't really a problem :)