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The suggestion by @xhochy of specifying only minimum version seems to work for now and is used in the current version 2.4.2. Since maintaining a contrib-package is quite some work (re-wiring all the internal imports of every module for each release), this issue is not that pressing and beneficial as first thought.
One possibility to avoid problems like #69 would be to include those essential parts like pbr and setuptools_scm directly into PyScaffold.
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