You're certainly right about people going outside the packaging system for Web applications, at least for the ones where they are following the development of the software and want the latest features as they get delivered. This isn't always a great experience, though: language-specific deployment systems may neglect things like proper integration with the system (you have to write your own init script or search for one on the net) and dependencies beyond the language ecosystem, leaving you having to manage a lot of separate software installations either manually or by leaning on various repositories that don't provide the same level of confidence that, say, the Debian repositories provide with all their safeguards.
I feel that those pushing language-specific software management neglect the fact that a lot of people deploying software are doing so without an intimate knowledge of (or enthusiasm for) the implementation technologies. For that audience, having a stream of updates from a reliable source is far more important than the absolute latest code coming from a collection of different repositories controlled by a range of differing language-specific tools.
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