Indeed. I myself am on Doom Emacs but I've increasingly been thinking of moving over to vanilla Emacs. I'm a bit worried about the transition period due to all the keybind differences but I'm sure it's not too bad.
Tell your agent what parts of Doom Emacs you actually use, and ask it to build a minimal init.el containing only those parts. You're probably only using ~2% of Doom, so the resulting init.el will likely only be a few hundred lines, and most of those lines will be comments and key bindings.
It won't be a perfect transition, but it will make it a lot smoother.
Don't get me wrong, I'm loving Doom and have used it full time for a few years now. But over time I've started being uncomfortable with the fact that I don't fully understand the editor, don't fully appreciate the difference between what comes in as part of vanilla Emacs and as a Doom feature, and I feel like I am depending on a huge bunch of code and configuration I might not really even need.
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've had multiple config bankruptcies over the years until settling down with Doom. I'm considered "experienced Emacsian" - built and published packages, etc. I'm still using Doom but only the core of it. I don't even consume almost any of its "official" modules - I have my custom ones instead. I have considered building my own config from scratch (yet again), but I like Doom's core macros - map!, add-hook!, defadvice!, undefadvice!, etc. I'd probably inevitably end up borrowing them and structuring my new config just like I already have, so I see no point.
> 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.
It won't be a perfect transition, but it will make it a lot smoother.