There are several reasons for this. I'll tell you the first few things that come to my mind.
Automatic package builders use heuristics to determine specific information. For example they "guess" the license of a module, which can get you into serious troubles as a distributor. They "guess" the build-dependencies. This usually works well for pure-perl modules with a complete PREREQ_PM list, but fails for almost any module which doesn't use pure-perl only.
Packages generated by those tools tend to be low-quality. They don't use common best-practices in packaging, they use outdated stuff like compatibility versions (debian/compat) and they have no clue about what documentation should be in the package and what shouldn't.
Beside that they are, at least in my experience, not very robust. Not only the generated packages are broken (do not build, install, work, whatever), even the tools itself croak from time to time, if they don't like the module they should package.
These might not be the most important things, but they might be enough to see that one shouldn't create debian source packages in a full automated fashion.
Nevertheless, even I use dh-make-perl and friends from time to time. Most perl packages look the same from the debian packagers point of view. This makes it possible to use dh-make-perl to do the boring things, like a first debian/rules version, etc. and concentrate on those things that the tools can't do for you: Checking the copyright information, finding a good package description, ...
HTH, Flo
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