Not needing to have Autotools installed is certainly a feature and not a design flaw, it is the entire purpose of the project and as i wrote near the end it is

Not needing to have Autotools installed is certainly a feature and not a design flaw, it is the entire purpose of the project and as i wrote near the end it is the reason i personally prefer using it compared to other projects. Also note that you can still regenerate configure scripts if you have Autotools installed, so it isn't like what you describe cannot be done with how Autotools are right now. According to a comment in the discussions i linked to, Debian already regenerates the configure scripts as part of their building process. The difference is that unlike other tools, you don't need to do that - for example i can easily download the source of some program with an outdated configure script on my main Linux PC, regenerate the script with my PC's version of Autotools and then copy the resulting package to another machine running -say- NetBSD that doesn't have Autotools (or any of its dependencies) installed and be able to build it there.