Incksape uses autopackage, Sciribus uses Cmake, most other packages still use ./configure followed by make. We are I fear headed for a kind of tower of Babel with install methods on Open source programs.
I don't think we are, for two reasons.
The first is that I remember when almost every project used the same build system, and that build system consisted of editing the Makefiles by hand for your platform. If you were lucky, the project's INSTALL file gave you hints on how to correctly set the make variables, and told you what libraries it depended on. If you were unlucky, you found out when make failed, and still couldn't tell whether it needed a library you didn't have or was just looking in the wrong place. I often complain about build systems being hard to use as a developer, but for a user it's definitely got much easier. A proliferation of build systems is better than none at all.
The second reason is simply that it doesn't matter if projects use different build systems, because they very rarely need to communicate with each other. The only cost in using projects with different build systems is that you have to have all their build systems installed rather than just one.