Aha; not so weird, after all. The Gambit built by Marc's script is built to run on the named target--in the case of the IPhoneSimulator version, it's intended to run on the IPhoneSimulator (duh!).
So what I needed to do was use the MacOSX version of Gambit to compile the Scheme sources against the IPhoneSimulator versions of the libraries, includes, and so forth.