A GMP user pointed out that the setups of as_ln_s include a fallback to "cp" if "ln" fails, but that the same isn't true of config.status when it sets up the AC_CONFIG_LINKS.
I don't have a set of actual circumstances where there's a problem, though it would seem that if it's necessary to fall back to a copy in one spot then very likely it is in both. I guess AC_CONFIG_LINKS describes itself as creating links, but any package depending on a link rather than a copy will already fail on a system where links don't work, so I imagine creating a copy in that case wouldn't make anything worse.