It seems that in many, many cases, we just to "adjust" a handful of the ennvars populated by ap_add_cgi_vars()... Right now, with my patch, we are doing it directly and explicitly in mod_proxy_fcgi. No doubt there are other places that need such special treatment as well.
One possibility would be to continue in that fashion... Another would be to add some sort of hook/callback/fixup to ap_add_cgi_vars() that modules like mod_include, mod_proxy_fcgi,... can register. The latter seems "cleaner", for some reason, but most likely overkill for the limited cases we are dealing with.