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well, you picked a bad example with Mozilla, as to my certain knowledge that compiles perfectly on a stock Mandrake box with the appropriate development packages installed, and I'd be amazed if that wasn't the case on other major distros. File structure on Linux distros pretty much is unified, at least for the purposes of building packages; static distro-packaged data in /usr, static user-built data in /usr/local, configuration in /etc, dynamic stuff in /var. Easy, and standard across distros. The need to rebuild comes from the use of non-compatible versions and packages of common libraries, not incompatible directory structures.
Replying to a post about SuSE-unique features, I could point out that Mandrake includes udev, devfs, hal and hotplug. And I don't believe SuSE actually includes Ximian GNOME, at least not yet.