I don't really care that much, I just personally find it annoying having so many different Unix-style trees. One of the reason it works on Unix is that everything is under the same root. On Windows, the convention seems to generally be to put stuff in logical(ly named) folders according to what's in them, that is with the exception of FOSS projects who can't be bothered to tailor the file system layout for the platform it's on :)

and especially if we want to use Autotools everywhere

That's not really related, it's not like Autotools is used to install anything.

P.S. It's only 5 lines, and it's in an area of the code designed specifically for this purpose.

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