> but implicitly will use A if present (thanks autoconf!)

When you want reproducibility, you need to specify what you want, not let the computer guess. Why can't you use Y/configure --without-A ? In the extreme case you can also version config.status.

One certainly can, but such is not default.

Things using autotools evolved to be “manual user friendly” in the sense that application features are automatically enabled based on auto detected libraries.

But for automated builds, all those smarts get in the way when the build environment is subject to variation.

In theory, the Yocto recipe will fully specify the application configuration regardless of how the environment varies…

Of course, in theory the most Byzantine build process will always function correctly too!