Negative Pricing in BOM

Summary:

We are storing negative prices for some of our items in Pricebook, so while configuring we are getting negative prices for these items and they are not being considered for total bom price. While in commerce , since we have written custom logic to handle the total prices , there is a price difference in configuration bom total and commerce total.Example : If a BOM has 5 parts with total price as 100$ and one part is -10$, in configuration BOM price is coming as 100$ while in commerce we are getting it as 90$.

Is there any way where we can handle this and there is no mismatch in Commerce and Config Prices.