### 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)

#ifdef TOOLS_ENABLED
	if (parent_skeleton) {
		Transform3D bone_transform(parent_skeleton->get_global_transform());
		if (-1 != bone_id) {
			bone_transform *= parent_skeleton->get_bone_global_pose(bone_id);
		}
		if (gizmo_move_joint) {
			bone_transform *= body_offset;
			set_joint_offset(bone_transform.affine_inverse() * get_global_transform());
		} else {
			set_body_offset(bone_transform.affine_inverse() * get_global_transform());
		}
	}
#endif
}
void PhysicalBone3D::_start_physics_simulation() {
	if (_internal_simulate_physics || !parent_skeleton) {
		return;
	}
	reset_to_rest_position();
	set_body_mode(PhysicsServer3D::BODY_MODE_RIGID);
	PhysicsServer3D::get_singleton()->body_set_collision_layer(get_rid(), get_collision_layer());
	PhysicsServer3D::get_singleton()->body_set_collision_mask(get_rid(), get_collision_mask());
	PhysicsServer3D::get_singleton()->body_set_collision_priority(get_rid(), get_collision_priority());
	PhysicsServer3D::get_singleton()->body_set_state_sync_callback(get_rid(), callable_mp(this, &PhysicalBone3D::_body_state_changed));
	set_as_top_level(true);
	_internal_simulate_physics = true;
}
void PhysicalBone3D::_stop_physics_simulation() {