I think the key phenomenon here is that software is non-portable by default, and portable through effort. If your problem is that the Linux code should use epoll() and the BSD code should use kqueue(), but OS X has quirks in its kqueue() implementation, and you need to fall back to poll() otherwise, autoconf will help... slightly. Then you need Sys V init scripts, or rc scripts, or launchd scripts, or... who even knows, unless you actually convince someone to port your project to that system.
So, you already have people testing and fixing bugs on other platforms, but now you tell them that they need to also learn M4 so they can write an Autoconf macro to test for some... thing... that you need which doesn't have a standard test. I'm not convinced that this makes my life any better.
Whether or not you like Autoconf, however, you have to agree that libtool has serious problems.
In my opinion, when possible, it is better to stuck to standards, and use just a Makefile for POSIX targets (it allows context detection) and a custom scripts or Makefiles for exotic platforms.
In the end, the reason for e.g. Autoconf, is the mess of different non-standard crazy stuff. Why not to agree a build standard base, at least for the C language and library handling?
Speaking as someone who was a system administrator responsible for compiling a large number of packages across a wide variety of platforms (let's see, SunOS, Solaris, AIX, Irix, Linux, and HP-UX, all at different versions at different times) through the '90s and early 2000s, autoconf made things much, much easier.
It doesn't help the developers any; each individual difference has to be identified by the developer. (My biggest complaint isn't that it's written in m4, but that there's no comprehensive list of what I need to do with it. That information makes up the m4 tests, but there was no documentation.)
Don't like libtool? http://www.fortran-2000.com/ArnaudRecipes/sharedlib.html
The bazaar model embraces the mess, believing that something spectacular will emerge. The cathedral model argues that coherence produces better results.
Both can point to successes. phk is arguing that the open source community has lost more than it has gained from accepting the bazaar as the one true way.
Even in the last ten years, where has the innovation in operating systems come from?
The CatB essay predates the book, and the idea predates UNIX.
As for libtool, anything that deals with shared libraries is inherently non-portable. The file extension they're created with and the compiler and linker flags to create them are entirely platform specific - POSIX won't help you there. (Also, a lot of libtool's hairyness exists because some older proprietary Unix systems don't support shared library dependencies.) If you're only planning on supporting open source OSes you don't actually need libtool though - their native toolchains are either the GNU one or something compatible with it, and include most of its functionality natively.
Compare POSIX to the Java spec: without Sun forcing coherence, "write once, run anywhere" would have died very early on, and we'd be saying the same thing about Java as you've just said about POSIX.
POSIX was just an example, and it is possible to write portable code using #ifdef. But you have to have a goal of writing portable code.
Re: libtool, most of the reason it's ever necessary is because of the historical rush and the incompatibilities created. Again, a single command line switch could handle that.
Still, plenty of software which has clearly only ever been built for Linux requires libtool. It's just the way things are done, just like autoconf. It works, poorly, inefficiently, fragile-ly -- and to most, mysteriously.
Appreciation for autoconf and libtool depends on one's position on the defeatism-pragmatism-idealism spectrum.
Yes, two ways. One way uses autoconf (and tests each individual option to see which branch of the ifdef to use) and the other uses Imake (and has a big, continuously maintained database of which option to use on each system).
So if you dropped SunOS, Tru64, HP-UX, IRIX, and AIX how many users would you use? How much of that configuration garbage would go away?