I think I found what I was looking for. There’s a table Qtmmkup which contains the material markup percentage by Class Code, and the field that’s displayed on the Worksheet for the markup percentage is a weighted average of all the Material that’s a part of the BOM.
My guess is the field QuoteQty.MaterialMarkUp was the field way back in the early versions of Vantage/Vista, and when Epicor introduced the ability to have material markup rates based on part class, just left the field out there.
I set the part class markups at various values, ran a query against QuoteMtl to get the cost per material (required quantity * Est Unit Cost), applied the markup rate based on the class ID of the material. With that, I ended up with the total Material Cost and Price, and was able to back into the weighted percentage.