Thats the term Stallman came up with when the first distributions (esspecially Debian) started to build up. It wasnt really popular even back than so he setteled in GNU/Linux as alternative which to this day is in the name of quit a lot distributions.
It was never the plan/intend to rename the Linux kernel itsself to either of those terms.
I don’t use autotools anymore for any of my private projects. It’s plain Makefiles for me simple and easy. But I usualy only target Linux.