Yes, indeed. This is a tricky one. The right-hand-side terms (ru, rv) for the 3D momentum equations are defined a vertical RHO-points. However, a k=0 index is added for the 2D/3D coupling in step2d. This k=0 index contains the vertically integrated forcing term. This term is needed in perfect restart. The solution here is to set the coordinates attribute to:
ru:coordinates = "lon_u lat_u s_w ocean_time" ;
rv:coordinates = "lon_v lat_v s_w ocean_time" ;
This is achieved in def_rst.F by passing -u3dvar and -v3dvar variables (Aval(5)) to routine def_var.