Since I have a template that I copy I was bit embarrassed that there might be
additional factors I hadn't reported, but no, the problem occurs with fresh
projects as well.

I uninstalled -13, installed -27, and started a new project, doing only two
things:
1) supplying the url (http://example.com/)
2) opening the site structure options and clicking ok to accept the default
(%h%p/%n%q.%t)

But even with just that the single html page is saved as index-2.html in the
root of the project, not under an example.com directory.

I'm using the 64-bit Windows version of WinHTTrack.