Peter,
I'm not an experienced boost user, but I am aware that much of boost is header-only
libraries. And it sounds like from your description above that your library installs
headers which also include this potentially broken
header<boost/exception_ptr.hpp>. The community would need to chime in here,
but for my projects I don't install the generated config.h or a subset
public_config.h like you have done, but since you already have that capability it
would probably be little effort for you to extend public_config.h with an AC_DEFINE
of the result of your test and then include your public_config.h from the top of your
installed headers.