Of course it can. It can be easier, faster and more failproof. Hacking this together in a shell script that tries to run the same on 50 slightly incompatible shells from the 70's is just about the worst way to solve the configuration problems present in compiling software.
The autoconf/automake solution is just a big ball of horribly written duck tape over make, which while a nice hack for very small projects, is surpassed by just about any other solution available today, bar just invoking the compiler and linker directly. That's goes even for single-file "hello world" programs.
It's also completely unmaintainable, which is why no one even bothers trying to fix the ~10 completely irrelevant compilers it checks for even when compiling a pure C program.
That's assuming you're using the GNU autoshit packages, of course. If you wrote your own small, clean and easily modifiable configure and make file, then good for you, but the ./configure could probably be ommited.