program-prefix and AC_CHECK* macros, etc...

[ceez]

I'm doing some contracting and for various reasons, my
client has been using a customized prefix and program-prefix
to carefully isolate their hacked binaries and libraries
from other versions for some opensource packages.

I started reading the autoconf/autotools documentation
expecting there be  some way of have an AC_CHECK macro (e.g.
AC_CHECK_LIB) perform a  search with these customized prefix
and/or program-prefix (or any of the other program-transform
options).  The former can be tweaked with adjustments to the
Environment variables PATH, LIBS, etc..   But I was
surprised to discover that this doesn't quite seem to be so
simple if any of the program-transform features have been
used.

Is there some generally accepted or preferred way to have
configure handle program-prefix/suffix/transform
customizations already present on the machine?