I think a lot of it has to do with the challenges of validating changes to aircraft as safe. Additionally, the B-52 is relatively simple and inexpensive to operate.
As a lay person I imagine that the high wing of a B-52 vs the low wing of a modern Boeing might have something to do with center of gravity given the relative density and dynamic weight changes of bombs during a sortie vs stable passengers and luggage on a flight.
Since aircraft operate at much higher speeds than what we normal humans are accustomed to on a daily basis, there are significant concerns having to do with things like vibration [0] that may not be obvious.
That isn't to say that people aren't trying to reuse more commodity hardware over bespoke. For example, I understand that the P-8 Poseidon [1] is considered a successful program. It uses the 737 frame and does launch munitions, albeit not as many as a dedicated bomber aircraft.
Your idea of taking a sawsall to make a bomb bay door is not far off from the C-130 Harvest Hawk, which mounts bomb racks to existing cargo ramps.
0. The engineering required to fly fast (GVT): https://www.youtube.com/watch?v=sZGo-R2mtb8
1. https://en.wikipedia.org/wiki/Boeing_P-8_Poseidon
2. https://en.wikipedia.org/wiki/Lockheed_Martin_KC-130#Harvest...