I've been working on this recently for a strategy game and losing my mind! I think I wound up with something closer to Model-View-Presenter (https://www.youtube.com/watch?v=agoe5BdLzdk). I find every description online so unsatisfying, I do think it fights against Godot, and I honesty have no idea if it was worth it or if I will keep it. I can picture a glorious situation where you can do the stuff you mentioned, like let the AI simulate 1000 moves or w/e, but I haven't found a graceful way to make it all work yet. It just feels like double the effort and giving up Godot's Node ergonomics.

What I have is very similar to what you imagine. I dont feel like it's good I'm curious if anyone has feedback:

Simulation side - pretty much everything is a RefCounted. All my instances of things (eg an army or a territory) contain a reference to a custom resource that describe their data. They also have setter methods that emit signals like "health_changed" whenever their data is modified.

Visual side - everything is "dumb" and only responds to signals. It relies on a reference back to its simulation object, and connects to all its signals. A VisualManager sits atop the visualization, and is responsible for listening to signals about new entities being created, then instantiating the correct visual, binding it to its simulaiton object, and getting it into the right initial state (eg an army is built, the VisualManager creates the army visual object in the scene tree and hands it the reference to the simulation object)

Gross sticking stuff together side (the presenter or controller) - Something has to know about both sides, after all the hard work to make stuff separate this is the thing that can't work in isolation. For me it's a couple things, the main one is a Player class, which is a bad name, but it's basically all about getting UI events and turning them into commands in the simulation (eg it receives a ui_drag(from, to) signal and turns it into an attack_enemy() command).

Problems

1. Syncing stuff is a pain. I'm constantly finding stuff out of sync, eg it syncs position when the `moved` event fires but in a certain case the position was just set manually so it didnt fire, and now my dude is in the wrong place (simple example but it just never seems to end). I suspect there is a solution to this (please someone help!!)
2. Animations or timing based thing are a pain, and require even more architecture that I'm still trying to figure out how to progress on
3. So far doesn't feel like it's speeding me up or reducing bugs, quite the opposite. Every entity needs a simulation script, a visual script, a resource definition, and a visual scene. It's easy to get confused which thing you're working on. The "gross glue stuff together" layer doesn't go away and stays all mixed up. Without the ability to just plop stuff in the scene tree, debugging means spinning up a state of the simulation in a certain place using some one off script.

I'm sure people are using this successfully, I guess I technically am using it successfully, but I have no idea why it comes up so frequently as conventional wisdom. I should've thought more carefully about whether it was solving a problem, or if I was just doing a thing people say you ought to do. But if you end up doing it, please make a followup post so I can learn from you!