For sure. Major misalignment is more of a problem when switching from the more forgiving production line rope seal to the neoprene. Some of the rope seals even leaked when new.
we switched a neo seal on the hemi (back in the day) , just for ease of install. , but never had a problem on it either way , street hemi`s were machined "right" , never found one thing that wasn`t like the factory said ir was ...