The rules are different for commercial aviation and for the military. The goal of commercial aviation is to get people to their destination, as safely and cheaply as possible, you don't have to fight against an enemy. As a result, commercial aviation is not very creative. They tend to use proven designs and incremental improvement.
Making a civilian flying wing aircraft will be a certification nightmare, which may involve several full-scale prototypes, a new kind of training for pilots, etc... It is a world where there is still a switch for the "no smoking" sign in the cockpit that doesn't do anything because all flights are non smoking now. Removing the button would require re-qualification and it is easier to leave it there.
The B737-MAX fiasco is another illustration. Just look at how far their went just to limit change...
I'm not saying that a flying wing commercial aircraft can't be done, but I have a feeling that the placement of passengers won't be the biggest issue.