# byte-compile your init.el, then
emacs     # init.el is compiled to native code, and user-init-file =>
init.el
C-x C-c
emacs     # user-init-file => points to init-*-*.eln

Which I imagine is unintended, as there are other places in the code (for
example, custom) that expect user-init-file to point to an .el.

Note: The above recipe is entirely reproducible in my system, as long as
running Emacs native-compiles init.el. I add this caveat because I suppose
there's some size/complexity threshold to trigger the native compilation (a
one-line init.el[c] is not native-compiled, for example).