I actually agree with PHK, in the fact that "craftsmanship" has gone to the wayside. Atleast in the sense of a "finished product, including the compilation process". Though I tend to believe it is not the "way of the bazaar one should blame - more that of the ever increasing pressure to "get something out", and since the std. autotools mess "works" - people just leave it at that - and focus on their projects goal, instead of bothering with those details (they only scratch their own itch in that sense).
I bet there's just as many well-educated programmers, that do the exact same half-assed build-thing and are just glad it works, so they can focus on what their managers want them to deliver.
And since it's Open Source - I'm sure most of the projects would welcome an update to their build process, to help the situation.. anyone?