You don't need to add mcfly bash integration to your .bashrc manually. Remove it from home.packages and instead enable the home-manager module with programs.mcfly.enable = true;. That's all you need to do, it has a enableBashIntegration setting that's true by default. Same for atuin, programs.atuin.enable = true; is enough.

It's an habit you have to learn when switching to nix, check first if there is a module for the program you want to install before resorting to home.packages or environment.systemPackages.