I think the uncertainty had more to do with the implosion mechanism than nuclear physics. The ability to simulate the hydrodynamics of an imploding sphere was

I think the uncertainty had more to do with the implosion mechanism than nuclear physics. The ability to simulate the hydrodynamics of an imploding sphere was obviously pretty limited in 1945, and while Los Alamos devised a series of pretty ingenious experiments to test how symmetrical such implosions could be made, for obvious reasons they had to use mock setups with metals other than Plutonium. So there seems to have been a fair amount of skepticism that such a mechanism could be made to work right up until Trinity.