My understanding of site-start.el is that it actually loads all the Emacs packages that are listed in my Guix profile. Which means that my package list matters. Here is a minimal containerized example that creates a process avalanche:
guix shell -C emacs emacs-ido-completing-read+ \ -- emacs --batch --eval="(print load-path)" ido-completing-read+ is a rather small Emacs package, and I don't see anything obvious in it that could cause trouble with native compilation. But more importantly, I think no package should be able to cause the behavior that I observe. Cheers Konrad.