See log file, generated in user:// I included a sample log file. It looks like at least Sprite3D is causing the delay issue. These logs should show the difference in interval between instancing scenes from inside a thread. You can un-check "use thread" on the root node to compare.
norlowski/GodotThreadLoadExample
Minimal example to show issues with some nodes being instanced from within a thread. in godot
GDScriptMIT