The author's point is to do <em>without</em> a configure step entirely, not write your own.
A standard Makefile is perfectly capable of implementing these things in a manner which is clean, reasonably portable and without the level of indirection that makes things hard to debug.
My own experience is that autotools has evolved to feel less standard than the modern platforms it purports to smooth over the differences in; I seem to frequently find that I can't generate a 'configure' for a 3rd party software or libraries from Git repositories because I of the wrong autotools versions. Efforts to investigate this by unpicking the various macros etc. provided in the build have almost always been unsuccessful, leaving me building from distributed .tar.gz files. With something that feels like such a moving target after 30 years, I'm glad to see people realising the benefit of a simple Makefile that's easy to customise for the edge cases.