### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

state.current_instance_buffer_index++;
	if (int(state.current_instance_buffer_index) < state.canvas_instance_data_buffers[state.current_data_buffer_index].instance_buffers.size()) {
		
		return;
	}
	GLuint new_buffer;
	glGenBuffers(1, &new_buffer);
	glBindBuffer(GL_ARRAY_BUFFER, new_buffer);
	GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_ARRAY_BUFFER, new_buffer, data.max_instance_buffer_size, nullptr, GL_STREAM_DRAW, "Batch UBO[" + itos(state.current_data_buffer_index) + "][" + itos(state.canvas_instance_data_buffers[state.current_data_buffer_index].instance_buffers.size()) + "]");
	state.canvas_instance_data_buffers[state.current_data_buffer_index].instance_buffers.push_back(new_buffer);
	glBindBuffer(GL_ARRAY_BUFFER, 0);
}
void RasterizerCanvasGLES3::set_time(double p_time) {