Dear Stefano - Thanks very much for your sympathetic reply on the directory permissions issue. As we haven't heard back further after a few days, I'd suggest going forward with plan 2.
You found that plan 2 was formerly proposed at <http://lists.gnu.org/archive/html/bug-automake/2003-05/msg00011.html>. You suspected that it wasn't applied. I believe that actually, it was applied, but then reverted because it broke someone's build. As I wrote in a followup to my original post:
Followup -- see this thread from 2004:
http://www.digipedia.pl/usenet/thread/16496/9413/
Looks like at one point, someone fixed this problem in the way I suggested. But then a user on that thread found directory permissions of 755 too restrictive, which may have gotten the fix removed.
One way to make everyone happy might be to ensure that a newly created directory has permissions of *at least* 755. (Although it's a bit peculiar to handle directories this way when files are standardly 644 ...)