It won't be a perfect transition, but it will make it a lot smoother.
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.
Selfishly I wasn't willing to spend the time to master Emacs proper back then, but with the LLM craze now I find it much easier to hack on my configs.
> I don't fully understand the editor
Going vanilla will not help you there - well, not completely anyway. Moreover, it may even obscure some features that were easily accesible before.
> I don't fully appreciate the difference between what comes in as part of vanilla Emacs and as a Doom feature
That is not very difficult - learn how to use built-in features - profiler, edebug, describe-, apropos-, hooks and advising, etc.; Start writing Elisp code (with understanding it). In the end, it won't really matter - whatever runs in your Emacs, there's always a way to get to the source. And if you ever need to disable any feature of Doom - there are multiple ways to do that.