Are you saying the cost etc. allocations in Boeing are underrepresenting the importance of commercial? Not quite sure I understand.
There's still quite a few brass in the US military who came of age in the immediate post-Vietnam era and remember the BUFFs being the core of the US bomber fleet, and will subconsciously favor Boeing over anything else. That means a better (though not guaranteed) likelihood of winning a contract.
The issue is, a lot of their offerings for things like tankers, AWACS, general transport, VIP transit, etc. are based on airliners.