IMO it’s probably due to the choices leading to a twin boom in the first place. Most are due to engine size and so to put the cockpit in they would have to place it very far back. This would make for very poor visibility for a fighter. It also means the displaced guns have to either go into the wing or into a new nacelle. Which means that unless they’re also in the same boom as the cockpit, you now have to either converge their fire or come up with some very complex aiming. At which point it likely becomes easier to just add the middle cockpit/weapons pod.

As for why the twin mustang didn’t happen sooner, it kinda barely happened at all. The only real reason for it was due to the B-29 out ranging current long range escorts. Prior increases in bomber range could be met by conventional improvements to escort fighters. It was kept in service more due to its late design meaning it was still a very modern prop plane as the US was caught transitioning to jets.