Done this exact thing. Fed an agent my actual keybindings and `M-x` history, let it regenerate a lean init.el. Two notes from the other side of it. It's great at the 2% you named, but it silently drops the muscle-memory stuff you never think about: which-key, the half-configured LSP, that one hydra. Diff the old and new against a day of real editing, not against your memory of what you use.
The bigger thing. "Ask the agent to build it" is fine here because init.el is read-only damage. Worst case it writes a file you `git diff` before trusting. That's the safe end of the spectrum. The instinct breaks the moment the same agent is touching things you can't cheaply inspect: package installs, shell-outs in a hook, anything with a side effect off your disk.
The lesson I keep relearning building this stuff: an audit log after the fact tells you what broke, it doesn't stop it. What you actually want is a capability check before the agent acts. This run is allowed to write `~/.config`, not to curl-pipe-sh. Plus a trail you can't quietly rewrite later, a hash chain, not a log file anyone with write access can edit. For an init.el that's overkill. For an agent you'd let near `apt` or your dotfiles repo, it's the whole game.