The list of things autoconf and automake do for you in a consistent fashion is endless, and scons does next to none of them. Neither do projects which use scons, and some of those facilities (notably CFLAGS overriding and install-time prefix or DESTDIR support) are essential for any project to be easily packaged. The best you'll get with scons is a means of doing this which is inconsistent for every single package: not very useful.
(cmake used to be bad in this regard too, but is much better these days, though it still supports no analogue of the useful site-config files, so you need wrapper scripts to simulate that. waf appears to provide some of them, but in a profoundly non-extensible fashion, apparently under the belief that if you want to configure CFLAGS the same way across many packages, you'll be happy to hack the waf scripts for every one of them to ensure they're not overriding it. Wrong.)
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