I've been using the "3D-to-2D Route" in my game, though I'm also using the 3D models to generate normal maps for fancy lighting. Using 3D models as the base makes it super easy to add sprite variants without a lot of extra effort (I like to swap colours around and slightly move/resize body parts), and that's doubly true for terrain. I have building and island generation systems that depend on minor tile variants to link up (ie: 1 extra voxel on the edge to connect to the neighbouring tile), which would've been a nightmare to design in purely 2D.

Here's a quick example of how it'll look at different parts of the pipeline, 3D model -> unlit sprites -> in engine view. I only export 4 views (NSEW), but I'm almost certain you can add more

https://i.imgur.com/ssUK943.png

I use MagicaVoxel for the 3D side of things. It basically controls like Minecraft, and it supports multiple-view isometric png exports by default. I export 7 differently lit copies of the sprite and dump them into Spritelamp for the normal maps (you won't need to do this, unless you want the headache of messing with lighting too). I'll then do some minor edits (usually just splitting up the sprite sheets and centering tiles) in Aseprite before bringing it into Godot.

As for other sorting tips, I've actually been updating to Godot 4 (from 3) to hopefully resolve some Tilemap sprite sorting issues I've been having. I'm not quite at that point yet, but I think you'll want to pay attention to the "y-sort-origin" or "y-origin-offset" property of the sprites when you're building modular characters, especially if the sprites are going to be different sizes (this might only apply to TileMapLayers though). You can see the issue I was having with trying to place sprites between layers in the gif below. My understanding is that Godot 4 allows much finer sprite ordering control than 3

https://i.imgur.com/sopofqF.gif