Sounds like all these starter packs need to use purely functional package managers like straight.el (or the newer elpaca) who has the ability to pin to exact commit hash of the third party packages. Afaik, Doom Emacs does exactly that, and it doesn't have such reproducibility issues?

Theoretically, another source of deviation might be different distros shipping different builds of Emacs using different flags, resulting in things like different graphics backend (like GTK vs pure X11). I am not sure if this is a legitimate concern in practice, but using something like Nix or Guix might eliminate even that.