> One downside to godot’s inheritance is everything is set up in code and decided at compile time instead?

That's not really the case because Godot can load scenes at runtime. The scene format itself (.tscn files) is text based[1] (which is also nice for version control) and could be edited by hand, then loaded into the game at runtime. Though since the Godot editor is open source and totally free it would probably be better just to ship that with the game. It's also really easy to extend so custom game centric plugins that modify the editor itself are also easy to write.

1: Here is a sample scene file, just to give a sense of the format:

    $ cat enemies/bandit/BanditSpread.tscn

    [gd_scene load_steps=2 format=2]

    [ext_resource path="res://enemies/bandit/BanditBase.tscn" type="PackedScene" id=1]

    [node name="BasicBandit" instance=ExtResource( 1 )]
    fire_period = 0.85

    [node name="VK-001" parent="Sprite" index="6"]
    visible = true

    [node name="LG-Anger" parent="Sprite" index="8"]
    modulate = Color( 1, 3.1875, 6, 1 )

    [node name="ProjectileWeapon" parent="Hardpoints" index="0"]
    projectile_spread_degrees = 60.0
    projectile_variance_degrees = 0.0
    num_projectiles_min = 6
    num_projectiles_max = 6