This article looks at how to create a structure for building and distributing applications, including heavily customized versions, and a simple way of disseminating the applications among a number of machines, manually or automatically, as easily as possible.
http://www.specifixinc.com/technology/
1) Package management and creating packages ain’t addressed (but is referred to at the resources link).
2) Cross-compiling ain’t explained.
While the idea of such hierarchy ain’t half that bad, especially if you compile a lot, this is also quite some work. First of all compiling from source by efinition although that depends per system. But especially regarding fine-tuning the configure flags. However at the moment you got the best configure flags for a package and/or version of a package which suit your needs its smart to write them down (and e.g. use them in this hierarchy as part of a scipt). Using that way, it all becomes a lot easier to admin.