### Godot version

Godot 4 stable and Godot 3.x LTS

### System information

Fedora linux

### Issue description

If you use some custom logic inside _integrate_forces() to alter the state linear velocity and there is any reference to linear_velocity in physics process, the result in godot 3.5 is that it moves just a little bit, while in godot 4 is totally still.

### Steps to reproduce

For the example i created a simple scene in which i apply a force on the linear velocity in  _integrate_forces()  and added a line that add zero to it in physics process. You will not see any move, but it will work fine if you comment the line adding zero.


### Minimal reproduction project

[PhysicsBugReproduction.zip](https://github.com/godotengine/godot/files/12139772/PhysicsBugReproduction.zip)

if (!simulate_physics || !_internal_simulate_physics) {
		return;
	}
	linear_velocity = p_state->get_linear_velocity();
	angular_velocity = p_state->get_angular_velocity();
	GDVIRTUAL_CALL(_integrate_forces, p_state);
	//
	Transform3D global_transform(p_state->get_transform());
	set_ignore_transform_notification(true);
	set_global_transform(global_transform);
	set_ignore_transform_notification(false);
	_on_transform_changed();
	// 
	if (parent_skeleton) {
		if (-1 != bone_id) {
			parent_skeleton->set_bone_global_pose_override(bone_id, parent_skeleton->get_global_transform().affine_inverse() * (global_transform * body_offset_inverse), 1.0, true);
		}
	}
}
void PhysicalBone3D::_bind_methods() {