Personally I'd say we have better things to work on than maintaining multiple buildsystems for notmuch. Or than resolving possible packaging bugs originating in the use of different buildsystems.
GNU has a very wide install bas, it's has a low footprint, and it happened to be the choice of the initial developers. All of this makes it the best choice imo. While I don't want to start a discussion on the merits of various buildsystems, I'll mention that, in my role as a packager, I'd choose just about anything over scons. My 2 cents, Ingmar -- Exherbo KDE, X.org maintainer